diff --git a/container_opts.go b/container_opts.go
index b8d334638..96ba75812 100644
--- a/container_opts.go
+++ b/container_opts.go
@@ -2,10 +2,12 @@ package containerd
 
 import (
 	"context"
+	"time"
 
 	"github.com/containerd/containerd/containers"
 	"github.com/containerd/containerd/errdefs"
 	"github.com/containerd/containerd/platforms"
+	"github.com/containerd/containerd/snapshot"
 	"github.com/containerd/typeurl"
 	"github.com/gogo/protobuf/types"
 	"github.com/opencontainers/image-spec/identity"
@@ -91,7 +93,11 @@ func WithNewSnapshot(id string, i Image) NewContainerOpts {
 			return err
 		}
 		setSnapshotterIfEmpty(c)
-		if _, err := client.SnapshotService(c.Snapshotter).Prepare(ctx, id, identity.ChainID(diffIDs).String()); err != nil {
+		labels := map[string]string{
+			"containerd.io/gc.root": time.Now().String(),
+		}
+		parent := identity.ChainID(diffIDs).String()
+		if _, err := client.SnapshotService(c.Snapshotter).Prepare(ctx, id, parent, snapshot.WithLabels(labels)); err != nil {
 			return err
 		}
 		c.SnapshotKey = id
@@ -120,7 +126,11 @@ func WithNewSnapshotView(id string, i Image) NewContainerOpts {
 			return err
 		}
 		setSnapshotterIfEmpty(c)
-		if _, err := client.SnapshotService(c.Snapshotter).View(ctx, id, identity.ChainID(diffIDs).String()); err != nil {
+		labels := map[string]string{
+			"containerd.io/gc.root": time.Now().String(),
+		}
+		parent := identity.ChainID(diffIDs).String()
+		if _, err := client.SnapshotService(c.Snapshotter).View(ctx, id, parent, snapshot.WithLabels(labels)); err != nil {
 			return err
 		}
 		c.SnapshotKey = id
diff --git a/content/helpers.go b/content/helpers.go
index 1c1087057..af05d0688 100644
--- a/content/helpers.go
+++ b/content/helpers.go
@@ -69,7 +69,7 @@ func WriteBlob(ctx context.Context, cs Ingester, ref string, r io.Reader, size i
 // the size or digest is unknown, these values may be empty.
 //
 // Copy is buffered, so no need to wrap reader in buffered io.
-func Copy(ctx context.Context, cw Writer, r io.Reader, size int64, expected digest.Digest) error {
+func Copy(ctx context.Context, cw Writer, r io.Reader, size int64, expected digest.Digest, opts ...Opt) error {
 	ws, err := cw.Status()
 	if err != nil {
 		return err
@@ -96,7 +96,7 @@ func Copy(ctx context.Context, cw Writer, r io.Reader, size int64, expected dige
 		return err
 	}
 
-	if err := cw.Commit(ctx, size, expected); err != nil {
+	if err := cw.Commit(ctx, size, expected, opts...); err != nil {
 		if !errdefs.IsAlreadyExists(err) {
 			return errors.Wrapf(err, "failed commit on ref %q", ws.Ref)
 		}
diff --git a/gc/gc.go b/gc/gc.go
index b9c265044..e892be155 100644
--- a/gc/gc.go
+++ b/gc/gc.go
@@ -5,8 +5,25 @@
 // under certain use cases.
 package gc
 
+import (
+	"context"
+	"sync"
+)
+
+// Resourcetype represents type of resource at a node
+type ResourceType uint8
+
+// Node presents a resource which has a type and key,
+// this node can be used to lookup other nodes.
+type Node struct {
+	Type      ResourceType
+	Namespace string
+	Key       string
+}
+
 // Tricolor implements basic, single-thread tri-color GC. Given the roots, the
-// complete set and a refs function, this returns the unreachable objects.
+// complete set and a refs function, this function returns a map of all
+// reachable objects.
 //
 // Correct usage requires that the caller not allow the arguments to change
 // until the result is used to delete objects in the system.
@@ -15,11 +32,11 @@ package gc
 //
 // We can probably use this to inform a design for incremental GC by injecting
 // callbacks to the set modification algorithms.
-func Tricolor(roots []string, all []string, refs func(ref string) []string) []string {
+func Tricolor(roots []Node, refs func(ref Node) ([]Node, error)) (map[Node]struct{}, error) {
 	var (
-		grays     []string                // maintain a gray "stack"
-		seen      = map[string]struct{}{} // or not "white", basically "seen"
-		reachable = map[string]struct{}{} // or "block", in tri-color parlance
+		grays     []Node                // maintain a gray "stack"
+		seen      = map[Node]struct{}{} // or not "white", basically "seen"
+		reachable = map[Node]struct{}{} // or "block", in tri-color parlance
 	)
 
 	grays = append(grays, roots...)
@@ -29,9 +46,13 @@ func Tricolor(roots []string, all []string, refs func(ref string) []string) []st
 		id := grays[len(grays)-1] // effectively "depth first" because first element
 		grays = grays[:len(grays)-1]
 		seen[id] = struct{}{} // post-mark this as not-white
+		rs, err := refs(id)
+		if err != nil {
+			return nil, err
+		}
 
 		// mark all the referenced objects as gray
-		for _, target := range refs(id) {
+		for _, target := range rs {
 			if _, ok := seen[target]; !ok {
 				grays = append(grays, target)
 			}
@@ -41,14 +62,99 @@ func Tricolor(roots []string, all []string, refs func(ref string) []string) []st
 		reachable[id] = struct{}{}
 	}
 
+	return reachable, nil
+}
+
+// ConcurrentMark implements simple, concurrent GC. All the roots are scanned
+// and the complete set of references is formed by calling the refs function
+// for each seen object. This function returns a map of all object reachable
+// from a root.
+//
+// Correct usage requires that the caller not allow the arguments to change
+// until the result is used to delete objects in the system.
+//
+// It will allocate memory proportional to the size of the reachable set.
+func ConcurrentMark(ctx context.Context, root <-chan Node, refs func(context.Context, Node, func(Node)) error) (map[Node]struct{}, error) {
+	ctx, cancel := context.WithCancel(ctx)
+	defer cancel()
+
+	var (
+		grays = make(chan Node)
+		seen  = map[Node]struct{}{} // or not "white", basically "seen"
+		wg    sync.WaitGroup
+
+		errOnce sync.Once
+		refErr  error
+	)
+
+	go func() {
+		for gray := range grays {
+			if _, ok := seen[gray]; ok {
+				wg.Done()
+				continue
+			}
+			seen[gray] = struct{}{} // post-mark this as non-white
+
+			go func(gray Node) {
+				defer wg.Done()
+
+				send := func(n Node) {
+					wg.Add(1)
+					select {
+					case grays <- n:
+					case <-ctx.Done():
+						wg.Done()
+					}
+				}
+
+				if err := refs(ctx, gray, send); err != nil {
+					errOnce.Do(func() {
+						refErr = err
+						cancel()
+					})
+				}
+
+			}(gray)
+		}
+	}()
+
+	for r := range root {
+		wg.Add(1)
+		select {
+		case grays <- r:
+		case <-ctx.Done():
+			wg.Done()
+		}
+
+	}
+
+	// Wait for outstanding grays to be processed
+	wg.Wait()
+
+	close(grays)
+
+	if refErr != nil {
+		return nil, refErr
+	}
+	if cErr := ctx.Err(); cErr != nil {
+		return nil, cErr
+	}
+
+	return seen, nil
+}
+
+// Sweep removes all nodes returned through the channel which are not in
+// the reachable set by calling the provided remove function.
+func Sweep(reachable map[Node]struct{}, all <-chan Node, remove func(Node) error) error {
 	// All black objects are now reachable, and all white objects are
 	// unreachable. Free those that are white!
-	var whites []string
-	for _, obj := range all {
-		if _, ok := reachable[obj]; !ok {
-			whites = append(whites, obj)
+	for node := range all {
+		if _, ok := reachable[node]; !ok {
+			if err := remove(node); err != nil {
+				return err
+			}
 		}
 	}
 
-	return whites
+	return nil
 }
diff --git a/gc/gc_test.go b/gc/gc_test.go
index 94ad3dd27..c3c6a9590 100644
--- a/gc/gc_test.go
+++ b/gc/gc_test.go
@@ -1,30 +1,154 @@
 package gc
 
 import (
+	"context"
 	"reflect"
 	"testing"
 )
 
 func TestTricolorBasic(t *testing.T) {
 	roots := []string{"A", "C"}
-	all := []string{"A", "B", "C", "D", "E", "F", "G"}
+	all := []string{"A", "B", "C", "D", "E", "F", "G", "H"}
 	refs := map[string][]string{
 		"A": {"B"},
 		"B": {"A"},
 		"C": {"D", "F", "B"},
 		"E": {"F", "G"},
+		"F": {"H"},
 	}
 
-	unreachable := Tricolor(roots, all, lookup(refs))
-	expected := []string{"E", "G"}
+	expected := toNodes([]string{"A", "B", "C", "D", "F", "H"})
 
-	if !reflect.DeepEqual(unreachable, expected) {
-		t.Fatalf("incorrect unreachable set: %v != %v", unreachable, expected)
+	reachable, err := Tricolor(toNodes(roots), lookup(refs))
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	var sweeped []Node
+	for _, a := range toNodes(all) {
+		if _, ok := reachable[a]; ok {
+			sweeped = append(sweeped, a)
+		}
+	}
+
+	if !reflect.DeepEqual(sweeped, expected) {
+		t.Fatalf("incorrect unreachable set: %v != %v", sweeped, expected)
 	}
 }
 
-func lookup(refs map[string][]string) func(id string) []string {
-	return func(ref string) []string {
-		return refs[ref]
+func TestConcurrentBasic(t *testing.T) {
+	roots := []string{"A", "C"}
+	all := []string{"A", "B", "C", "D", "E", "F", "G", "H", "I"}
+	refs := map[string][]string{
+		"A": {"B"},
+		"B": {"A"},
+		"C": {"D", "F", "B"},
+		"E": {"F", "G"},
+		"F": {"H"},
+		"G": {"I"},
+	}
+
+	expected := toNodes([]string{"A", "B", "C", "D", "F", "H"})
+
+	ctx := context.Background()
+	rootC := make(chan Node)
+	go func() {
+		writeNodes(ctx, rootC, toNodes(roots))
+		close(rootC)
+	}()
+
+	reachable, err := ConcurrentMark(ctx, rootC, lookupc(refs))
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	var sweeped []Node
+	for _, a := range toNodes(all) {
+		if _, ok := reachable[a]; ok {
+			sweeped = append(sweeped, a)
+		}
+	}
+
+	if !reflect.DeepEqual(sweeped, expected) {
+		t.Fatalf("incorrect unreachable set: %v != %v", sweeped, expected)
 	}
 }
+
+func writeNodes(ctx context.Context, nc chan<- Node, nodes []Node) {
+	for _, n := range nodes {
+		select {
+		case nc <- n:
+		case <-ctx.Done():
+			return
+		}
+	}
+}
+
+func lookup(refs map[string][]string) func(id Node) ([]Node, error) {
+	return func(ref Node) ([]Node, error) {
+		return toNodes(refs[ref.Key]), nil
+	}
+}
+
+func lookupc(refs map[string][]string) func(context.Context, Node, func(Node)) error {
+	return func(ctx context.Context, ref Node, fn func(Node)) error {
+		for _, n := range toNodes(refs[ref.Key]) {
+			fn(n)
+		}
+		return nil
+	}
+}
+
+func toNodes(s []string) []Node {
+	n := make([]Node, len(s))
+	for i := range s {
+		n[i] = Node{
+			Key: s[i],
+		}
+	}
+	return n
+}
+
+func newScanner(refs []string) *stringScanner {
+	return &stringScanner{
+		i: -1,
+		s: refs,
+	}
+}
+
+type stringScanner struct {
+	i int
+	s []string
+}
+
+func (ss *stringScanner) Next() bool {
+	ss.i++
+	return ss.i < len(ss.s)
+}
+
+func (ss *stringScanner) Node() Node {
+	return Node{
+		Key: ss.s[ss.i],
+	}
+}
+
+func (ss *stringScanner) Cleanup() error {
+	ss.s[ss.i] = ""
+	return nil
+}
+
+func (ss *stringScanner) Err() error {
+	return nil
+}
+
+func (ss *stringScanner) All() []Node {
+	remaining := make([]Node, 0, len(ss.s))
+	for _, s := range ss.s {
+		if s != "" {
+			remaining = append(remaining, Node{
+				Key: s,
+			})
+		}
+	}
+	return remaining
+}
diff --git a/image.go b/image.go
index d333c44fa..b41037a16 100644
--- a/image.go
+++ b/image.go
@@ -2,11 +2,16 @@ package containerd
 
 import (
 	"context"
+	"fmt"
+	"time"
 
+	"github.com/containerd/containerd/content"
 	"github.com/containerd/containerd/images"
 	"github.com/containerd/containerd/platforms"
 	"github.com/containerd/containerd/rootfs"
+	"github.com/containerd/containerd/snapshot"
 	digest "github.com/opencontainers/go-digest"
+	"github.com/opencontainers/image-spec/identity"
 	ocispec "github.com/opencontainers/image-spec/specs-go/v1"
 	"github.com/pkg/errors"
 )
@@ -64,36 +69,68 @@ func (i *image) Unpack(ctx context.Context, snapshotterName string) error {
 		return err
 	}
 
-	sn := i.client.SnapshotService(snapshotterName)
-	a := i.client.DiffService()
-	cs := i.client.ContentStore()
+	var (
+		sn = i.client.SnapshotService(snapshotterName)
+		a  = i.client.DiffService()
+		cs = i.client.ContentStore()
 
-	var chain []digest.Digest
+		chain    []digest.Digest
+		unpacked bool
+	)
 	for _, layer := range layers {
-		unpacked, err := rootfs.ApplyLayer(ctx, layer, chain, sn, a)
+		labels := map[string]string{
+			"containerd.io/gc.root":      time.Now().UTC().Format(time.RFC3339),
+			"containerd.io/uncompressed": layer.Diff.Digest.String(),
+		}
+		lastUnpacked := unpacked
+
+		unpacked, err = rootfs.ApplyLayer(ctx, layer, chain, sn, a, snapshot.WithLabels(labels))
 		if err != nil {
-			// TODO: possibly wait and retry if extraction of same chain id was in progress
 			return err
 		}
-		if unpacked {
-			info, err := cs.Info(ctx, layer.Blob.Digest)
-			if err != nil {
+
+		if lastUnpacked {
+			info := snapshot.Info{
+				Name: identity.ChainID(chain).String(),
+			}
+
+			// Remove previously created gc.root label
+			if _, err := sn.Update(ctx, info, "labels.containerd.io/gc.root"); err != nil {
 				return err
 			}
-			if info.Labels == nil {
-				info.Labels = map[string]string{}
-			}
-			if info.Labels["containerd.io/uncompressed"] != layer.Diff.Digest.String() {
-				info.Labels["containerd.io/uncompressed"] = layer.Diff.Digest.String()
-				if _, err := cs.Update(ctx, info, "labels.containerd.io/uncompressed"); err != nil {
-					return err
-				}
-			}
 		}
 
 		chain = append(chain, layer.Diff.Digest)
 	}
 
+	if unpacked {
+		desc, err := i.i.Config(ctx, cs, platforms.Default())
+		if err != nil {
+			return err
+		}
+
+		rootfs := identity.ChainID(chain).String()
+
+		cinfo := content.Info{
+			Digest: desc.Digest,
+			Labels: map[string]string{
+				fmt.Sprintf("containerd.io/gc.ref.snapshot.%s", snapshotterName): rootfs,
+			},
+		}
+		if _, err := cs.Update(ctx, cinfo, fmt.Sprintf("labels.containerd.io/gc.ref.snapshot.%s", snapshotterName)); err != nil {
+			return err
+		}
+
+		sinfo := snapshot.Info{
+			Name: rootfs,
+		}
+
+		// Config now referenced snapshot, release root reference
+		if _, err := sn.Update(ctx, sinfo, "labels.containerd.io/gc.root"); err != nil {
+			return err
+		}
+	}
+
 	return nil
 }
 
diff --git a/metadata/content.go b/metadata/content.go
index 023d5d215..05064fdec 100644
--- a/metadata/content.go
+++ b/metadata/content.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"encoding/binary"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/boltdb/bolt"
@@ -11,6 +12,7 @@ import (
 	"github.com/containerd/containerd/errdefs"
 	"github.com/containerd/containerd/filters"
 	"github.com/containerd/containerd/labels"
+	"github.com/containerd/containerd/log"
 	"github.com/containerd/containerd/metadata/boltutil"
 	"github.com/containerd/containerd/namespaces"
 	digest "github.com/opencontainers/go-digest"
@@ -19,12 +21,13 @@ import (
 
 type contentStore struct {
 	content.Store
-	db transactor
+	db *DB
+	l  sync.RWMutex
 }
 
 // newContentStore returns a namespaced content store using an existing
 // content store interface.
-func newContentStore(db transactor, cs content.Store) content.Store {
+func newContentStore(db *DB, cs content.Store) *contentStore {
 	return &contentStore{
 		Store: cs,
 		db:    db,
@@ -59,6 +62,9 @@ func (cs *contentStore) Update(ctx context.Context, info content.Info, fieldpath
 		return content.Info{}, err
 	}
 
+	cs.l.RLock()
+	defer cs.l.RUnlock()
+
 	updated := content.Info{
 		Digest: info.Digest,
 	}
@@ -166,15 +172,25 @@ func (cs *contentStore) Delete(ctx context.Context, dgst digest.Digest) error {
 		return err
 	}
 
+	cs.l.RLock()
+	defer cs.l.RUnlock()
+
 	return update(ctx, cs.db, func(tx *bolt.Tx) error {
 		bkt := getBlobBucket(tx, ns, dgst)
 		if bkt == nil {
 			return errors.Wrapf(errdefs.ErrNotFound, "content digest %v", dgst)
 		}
 
-		// Just remove local reference, garbage collector is responsible for
-		// cleaning up on disk content
-		return getBlobsBucket(tx, ns).DeleteBucket([]byte(dgst.String()))
+		if err := getBlobsBucket(tx, ns).DeleteBucket([]byte(dgst.String())); err != nil {
+			return err
+		}
+
+		// Mark content store as dirty for triggering garbage collection
+		cs.db.dirtyL.Lock()
+		cs.db.dirtyCS = true
+		cs.db.dirtyL.Unlock()
+
+		return nil
 	})
 }
 
@@ -269,6 +285,9 @@ func (cs *contentStore) Abort(ctx context.Context, ref string) error {
 		return err
 	}
 
+	cs.l.RLock()
+	defer cs.l.RUnlock()
+
 	return update(ctx, cs.db, func(tx *bolt.Tx) error {
 		bkt := getIngestBucket(tx, ns)
 		if bkt == nil {
@@ -293,6 +312,9 @@ func (cs *contentStore) Writer(ctx context.Context, ref string, size int64, expe
 		return nil, err
 	}
 
+	cs.l.RLock()
+	defer cs.l.RUnlock()
+
 	var w content.Writer
 	if err := update(ctx, cs.db, func(tx *bolt.Tx) error {
 		if expected != "" {
@@ -346,6 +368,7 @@ func (cs *contentStore) Writer(ctx context.Context, ref string, size int64, expe
 		ref:       ref,
 		namespace: ns,
 		db:        cs.db,
+		l:         &cs.l,
 	}, nil
 }
 
@@ -354,9 +377,13 @@ type namespacedWriter struct {
 	ref       string
 	namespace string
 	db        transactor
+	l         *sync.RWMutex
 }
 
 func (nw *namespacedWriter) Commit(ctx context.Context, size int64, expected digest.Digest, opts ...content.Opt) error {
+	nw.l.RLock()
+	defer nw.l.RUnlock()
+
 	return update(ctx, nw.db, func(tx *bolt.Tx) error {
 		bkt := getIngestBucket(tx, nw.namespace)
 		if bkt != nil {
@@ -495,3 +522,61 @@ func writeInfo(info *content.Info, bkt *bolt.Bucket) error {
 
 	return bkt.Put(bucketKeySize, sizeEncoded)
 }
+
+func (cs *contentStore) garbageCollect(ctx context.Context) error {
+	lt1 := time.Now()
+	cs.l.Lock()
+	defer func() {
+		cs.l.Unlock()
+		log.G(ctx).WithField("t", time.Now().Sub(lt1)).Debugf("content garbage collected")
+	}()
+
+	seen := map[string]struct{}{}
+	if err := cs.db.View(func(tx *bolt.Tx) error {
+		v1bkt := tx.Bucket(bucketKeyVersion)
+		if v1bkt == nil {
+			return nil
+		}
+
+		// iterate through each namespace
+		v1c := v1bkt.Cursor()
+
+		for k, v := v1c.First(); k != nil; k, v = v1c.Next() {
+			if v != nil {
+				continue
+			}
+
+			cbkt := v1bkt.Bucket(k).Bucket(bucketKeyObjectContent)
+			if cbkt == nil {
+				continue
+			}
+			bbkt := cbkt.Bucket(bucketKeyObjectBlob)
+			if err := bbkt.ForEach(func(ck, cv []byte) error {
+				if cv == nil {
+					seen[string(ck)] = struct{}{}
+				}
+				return nil
+			}); err != nil {
+				return err
+			}
+		}
+
+		return nil
+	}); err != nil {
+		return err
+	}
+
+	if err := cs.Store.Walk(ctx, func(info content.Info) error {
+		if _, ok := seen[info.Digest.String()]; !ok {
+			if err := cs.Store.Delete(ctx, info.Digest); err != nil {
+				return err
+			}
+			log.G(ctx).WithField("digest", info.Digest).Debug("removed content")
+		}
+		return nil
+	}); err != nil {
+		return err
+	}
+
+	return nil
+}
diff --git a/metadata/db.go b/metadata/db.go
index aed6f1e9a..7ae293159 100644
--- a/metadata/db.go
+++ b/metadata/db.go
@@ -3,10 +3,13 @@ package metadata
 import (
 	"context"
 	"encoding/binary"
+	"strings"
+	"sync"
 	"time"
 
 	"github.com/boltdb/bolt"
 	"github.com/containerd/containerd/content"
+	"github.com/containerd/containerd/gc"
 	"github.com/containerd/containerd/log"
 	"github.com/containerd/containerd/snapshot"
 	"github.com/pkg/errors"
@@ -36,15 +39,32 @@ type DB struct {
 	db *bolt.DB
 	ss map[string]snapshot.Snapshotter
 	cs content.Store
+
+	// wlock is used to protect access to the data structures during garbage
+	// collection. While the wlock is held no writable transactions can be
+	// opened, preventing changes from occurring between the mark and
+	// sweep phases without preventing read transactions.
+	wlock sync.RWMutex
+
+	// dirty flags and lock keeps track of datastores which have had deletions
+	// since the last garbage collection. These datastores will will be garbage
+	// collected during the next garbage collection.
+	dirtyL  sync.Mutex
+	dirtySS map[string]struct{}
+	dirtyCS bool
+
+	// TODO: Keep track of stats such as pause time, number of collected objects, errors
+	lastCollection time.Time
 }
 
 // NewDB creates a new metadata database using the provided
 // bolt database, content store, and snapshotters.
 func NewDB(db *bolt.DB, cs content.Store, ss map[string]snapshot.Snapshotter) *DB {
 	return &DB{
-		db: db,
-		ss: ss,
-		cs: cs,
+		db:      db,
+		ss:      ss,
+		cs:      cs,
+		dirtySS: map[string]struct{}{},
 	}
 }
 
@@ -158,5 +178,134 @@ func (m *DB) View(fn func(*bolt.Tx) error) error {
 
 // Update runs a writable transation on the metadata store.
 func (m *DB) Update(fn func(*bolt.Tx) error) error {
+	m.wlock.RLock()
+	defer m.wlock.RUnlock()
 	return m.db.Update(fn)
 }
+
+func (m *DB) GarbageCollect(ctx context.Context) error {
+	lt1 := time.Now()
+	m.wlock.Lock()
+	defer func() {
+		m.wlock.Unlock()
+		log.G(ctx).WithField("d", time.Now().Sub(lt1)).Debug("metadata garbage collected")
+	}()
+
+	var marked map[gc.Node]struct{}
+
+	if err := m.db.View(func(tx *bolt.Tx) error {
+		ctx, cancel := context.WithCancel(ctx)
+		defer cancel()
+
+		roots := make(chan gc.Node)
+		errChan := make(chan error)
+		go func() {
+			defer close(errChan)
+			defer close(roots)
+
+			// Call roots
+			if err := scanRoots(ctx, tx, roots); err != nil {
+				cancel()
+				errChan <- err
+			}
+		}()
+
+		refs := func(ctx context.Context, n gc.Node, fn func(gc.Node)) error {
+			return references(ctx, tx, n, fn)
+		}
+
+		reachable, err := gc.ConcurrentMark(ctx, roots, refs)
+		if rerr := <-errChan; rerr != nil {
+			return rerr
+		}
+		if err != nil {
+			return err
+		}
+		marked = reachable
+		return nil
+	}); err != nil {
+		return err
+	}
+
+	m.dirtyL.Lock()
+	defer m.dirtyL.Unlock()
+
+	if err := m.db.Update(func(tx *bolt.Tx) error {
+		ctx, cancel := context.WithCancel(ctx)
+		defer cancel()
+
+		nodeC := make(chan gc.Node)
+		var scanErr error
+
+		go func() {
+			defer close(nodeC)
+			scanErr = scanAll(ctx, tx, nodeC)
+		}()
+
+		rm := func(n gc.Node) error {
+			if n.Type == ResourceSnapshot {
+				if idx := strings.IndexRune(n.Key, '/'); idx > 0 {
+					m.dirtySS[n.Key[:idx]] = struct{}{}
+				}
+			} else if n.Type == ResourceContent {
+				m.dirtyCS = true
+			}
+			return remove(ctx, tx, n)
+		}
+
+		if err := gc.Sweep(marked, nodeC, rm); err != nil {
+			return errors.Wrap(err, "failed to sweep")
+		}
+
+		if scanErr != nil {
+			return errors.Wrap(scanErr, "failed to scan all")
+		}
+
+		return nil
+	}); err != nil {
+		return err
+	}
+
+	m.lastCollection = time.Now()
+
+	if len(m.dirtySS) > 0 {
+		for snapshotterName := range m.dirtySS {
+			log.G(ctx).WithField("snapshotter", snapshotterName).Debug("scheduling snapshotter cleanup")
+			go m.cleanupSnapshotter(snapshotterName)
+		}
+		m.dirtySS = map[string]struct{}{}
+	}
+
+	if m.dirtyCS {
+		log.G(ctx).Debug("scheduling content cleanup")
+		go m.cleanupContent()
+		m.dirtyCS = false
+	}
+
+	return nil
+}
+
+func (m *DB) cleanupSnapshotter(name string) {
+	ctx := context.Background()
+	sn, ok := m.ss[name]
+	if !ok {
+		return
+	}
+
+	err := newSnapshotter(m, name, sn).garbageCollect(ctx)
+	if err != nil {
+		log.G(ctx).WithError(err).WithField("snapshotter", name).Warn("garbage collection failed")
+	}
+}
+
+func (m *DB) cleanupContent() {
+	ctx := context.Background()
+	if m.cs == nil {
+		return
+	}
+
+	err := newContentStore(m, m.cs).garbageCollect(ctx)
+	if err != nil {
+		log.G(ctx).WithError(err).Warn("content garbage collection failed")
+	}
+}
diff --git a/metadata/db_test.go b/metadata/db_test.go
index e14242765..ff3e9cd15 100644
--- a/metadata/db_test.go
+++ b/metadata/db_test.go
@@ -1,11 +1,31 @@
 package metadata
 
 import (
+	"context"
 	"encoding/binary"
+	"fmt"
+	"io"
+	"io/ioutil"
+	"math/rand"
+	"os"
+	"path/filepath"
+	"runtime/pprof"
 	"testing"
+	"time"
 
 	"github.com/boltdb/bolt"
+	"github.com/containerd/containerd/containers"
+	"github.com/containerd/containerd/content"
+	"github.com/containerd/containerd/content/local"
 	"github.com/containerd/containerd/errdefs"
+	"github.com/containerd/containerd/gc"
+	"github.com/containerd/containerd/images"
+	"github.com/containerd/containerd/namespaces"
+	"github.com/containerd/containerd/snapshot"
+	"github.com/containerd/containerd/snapshot/naive"
+	"github.com/gogo/protobuf/types"
+	digest "github.com/opencontainers/go-digest"
+	ocispec "github.com/opencontainers/image-spec/specs-go/v1"
 	"github.com/pkg/errors"
 )
 
@@ -176,3 +196,366 @@ func readDBVersion(db *bolt.DB, schema []byte) (int, error) {
 	}
 	return version, nil
 }
+
+func TestMetadataCollector(t *testing.T) {
+	mdb, cs, sn, cleanup := newStores(t)
+	defer cleanup()
+
+	var (
+		ctx = context.Background()
+
+		objects = []object{
+			blob(bytesFor(1), true),
+			blob(bytesFor(2), false),
+			blob(bytesFor(3), true),
+			blob(bytesFor(4), false, "containerd.io/gc.root", time.Now().String()),
+			newSnapshot("1", "", false, false),
+			newSnapshot("2", "1", false, false),
+			newSnapshot("3", "2", false, false),
+			newSnapshot("4", "3", false, false),
+			newSnapshot("5", "3", false, true),
+			container("1", "4"),
+			image("image-1", digestFor(2)),
+		}
+		remaining []gc.Node
+	)
+
+	if err := mdb.Update(func(tx *bolt.Tx) error {
+		for _, obj := range objects {
+			node, err := create(obj, tx, cs, sn)
+			if err != nil {
+				return err
+			}
+			if node != nil {
+				remaining = append(remaining, *node)
+			}
+		}
+		return nil
+	}); err != nil {
+		t.Fatalf("Creation failed: %+v", err)
+	}
+
+	if err := mdb.GarbageCollect(ctx); err != nil {
+		t.Fatal(err)
+	}
+
+	var actual []gc.Node
+
+	if err := mdb.View(func(tx *bolt.Tx) error {
+		nodeC := make(chan gc.Node)
+		var scanErr error
+		go func() {
+			defer close(nodeC)
+			scanErr = scanAll(ctx, tx, nodeC)
+		}()
+		for node := range nodeC {
+			actual = append(actual, node)
+		}
+		return scanErr
+	}); err != nil {
+		t.Fatal(err)
+	}
+
+	checkNodesEqual(t, actual, remaining)
+}
+
+func BenchmarkGarbageCollect(b *testing.B) {
+	b.Run("10-Sets", benchmarkTrigger(10))
+	b.Run("100-Sets", benchmarkTrigger(100))
+	b.Run("1000-Sets", benchmarkTrigger(1000))
+	b.Run("10000-Sets", benchmarkTrigger(10000))
+}
+
+func benchmarkTrigger(n int) func(b *testing.B) {
+	return func(b *testing.B) {
+		mdb, cs, sn, cleanup := newStores(b)
+		defer cleanup()
+
+		objects := []object{}
+
+		// TODO: Allow max to be configurable
+		for i := 0; i < n; i++ {
+			objects = append(objects,
+				blob(bytesFor(int64(i)), false),
+				image(fmt.Sprintf("image-%d", i), digestFor(int64(i))),
+			)
+			lastSnapshot := 6
+			for j := 0; j <= lastSnapshot; j++ {
+				var parent string
+				key := fmt.Sprintf("snapshot-%d-%d", i, j)
+				if j > 0 {
+					parent = fmt.Sprintf("snapshot-%d-%d", i, j-1)
+				}
+				objects = append(objects, newSnapshot(key, parent, false, false))
+			}
+			objects = append(objects, container(fmt.Sprintf("container-%d", i), fmt.Sprintf("snapshot-%d-%d", i, lastSnapshot)))
+
+		}
+
+		// TODO: Create set of objects for removal
+
+		var (
+			ctx = context.Background()
+
+			remaining []gc.Node
+		)
+
+		if err := mdb.Update(func(tx *bolt.Tx) error {
+			for _, obj := range objects {
+				node, err := create(obj, tx, cs, sn)
+				if err != nil {
+					return err
+				}
+				if node != nil {
+					remaining = append(remaining, *node)
+				}
+			}
+			return nil
+		}); err != nil {
+			b.Fatalf("Creation failed: %+v", err)
+		}
+
+		// TODO: reset benchmark
+		b.ResetTimer()
+		//b.StopTimer()
+
+		labels := pprof.Labels("worker", "trigger")
+		pprof.Do(ctx, labels, func(ctx context.Context) {
+			for i := 0; i < b.N; i++ {
+
+				// TODO: Add removal objects
+
+				//b.StartTimer()
+
+				if err := mdb.GarbageCollect(ctx); err != nil {
+					b.Fatal(err)
+				}
+
+				//b.StopTimer()
+
+				//var actual []gc.Node
+
+				//if err := db.View(func(tx *bolt.Tx) error {
+				//	nodeC := make(chan gc.Node)
+				//	var scanErr error
+				//	go func() {
+				//		defer close(nodeC)
+				//		scanErr = scanAll(ctx, tx, nodeC)
+				//	}()
+				//	for node := range nodeC {
+				//		actual = append(actual, node)
+				//	}
+				//	return scanErr
+				//}); err != nil {
+				//	t.Fatal(err)
+				//}
+
+				//checkNodesEqual(t, actual, remaining)
+			}
+		})
+	}
+}
+
+func bytesFor(i int64) []byte {
+	r := rand.New(rand.NewSource(i))
+	var b [256]byte
+	_, err := r.Read(b[:])
+	if err != nil {
+		panic(err)
+	}
+	return b[:]
+}
+
+func digestFor(i int64) digest.Digest {
+	r := rand.New(rand.NewSource(i))
+	dgstr := digest.SHA256.Digester()
+	_, err := io.Copy(dgstr.Hash(), io.LimitReader(r, 256))
+	if err != nil {
+		panic(err)
+	}
+	return dgstr.Digest()
+}
+
+type object struct {
+	data    interface{}
+	removed bool
+	labels  map[string]string
+}
+
+func create(obj object, tx *bolt.Tx, cs content.Store, sn snapshot.Snapshotter) (*gc.Node, error) {
+	var (
+		node      *gc.Node
+		namespace = "test"
+		ctx       = namespaces.WithNamespace(context.Background(), namespace)
+	)
+
+	switch v := obj.data.(type) {
+	case testContent:
+		ctx := WithTransactionContext(ctx, tx)
+		expected := digest.FromBytes(v.data)
+		w, err := cs.Writer(ctx, "test-ref", int64(len(v.data)), expected)
+		if err != nil {
+			return nil, errors.Wrap(err, "failed to create writer")
+		}
+		if _, err := w.Write(v.data); err != nil {
+			return nil, errors.Wrap(err, "write blob failed")
+		}
+		if err := w.Commit(ctx, int64(len(v.data)), expected, content.WithLabels(obj.labels)); err != nil {
+			return nil, errors.Wrap(err, "failed to commit blob")
+		}
+		if !obj.removed {
+			node = &gc.Node{
+				Type:      ResourceContent,
+				Namespace: namespace,
+				Key:       expected.String(),
+			}
+		}
+	case testSnapshot:
+		ctx := WithTransactionContext(ctx, tx)
+		if v.active {
+			_, err := sn.Prepare(ctx, v.key, v.parent, snapshot.WithLabels(obj.labels))
+			if err != nil {
+				return nil, err
+			}
+		} else {
+			akey := fmt.Sprintf("%s-active", v.key)
+			_, err := sn.Prepare(ctx, akey, v.parent)
+			if err != nil {
+				return nil, err
+			}
+			if err := sn.Commit(ctx, v.key, akey, snapshot.WithLabels(obj.labels)); err != nil {
+				return nil, err
+			}
+		}
+		if !obj.removed {
+			node = &gc.Node{
+				Type:      ResourceSnapshot,
+				Namespace: namespace,
+				Key:       fmt.Sprintf("naive/%s", v.key),
+			}
+		}
+	case testImage:
+		image := images.Image{
+			Name:   v.name,
+			Target: v.target,
+			Labels: obj.labels,
+		}
+		_, err := NewImageStore(tx).Create(ctx, image)
+		if err != nil {
+			return nil, errors.Wrap(err, "failed to create image")
+		}
+	case testContainer:
+		container := containers.Container{
+			ID:          v.id,
+			SnapshotKey: v.snapshot,
+			Snapshotter: "naive",
+			Labels:      obj.labels,
+
+			Runtime: containers.RuntimeInfo{
+				Name: "testruntime",
+			},
+			Spec: &types.Any{},
+		}
+		_, err := NewContainerStore(tx).Create(ctx, container)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	return node, nil
+}
+
+func blob(b []byte, r bool, l ...string) object {
+	return object{
+		data: testContent{
+			data: b,
+		},
+		removed: r,
+		labels:  labelmap(l...),
+	}
+}
+
+func image(n string, d digest.Digest, l ...string) object {
+	return object{
+		data: testImage{
+			name: n,
+			target: ocispec.Descriptor{
+				MediaType: "irrelevant",
+				Digest:    d,
+				Size:      256,
+			},
+		},
+		removed: false,
+		labels:  labelmap(l...),
+	}
+}
+
+func newSnapshot(key, parent string, active, r bool, l ...string) object {
+	return object{
+		data: testSnapshot{
+			key:    key,
+			parent: parent,
+			active: active,
+		},
+		removed: r,
+		labels:  labelmap(l...),
+	}
+}
+
+func container(id, s string, l ...string) object {
+	return object{
+		data: testContainer{
+			id:       id,
+			snapshot: s,
+		},
+		removed: false,
+		labels:  labelmap(l...),
+	}
+}
+
+type testContent struct {
+	data []byte
+}
+
+type testSnapshot struct {
+	key    string
+	parent string
+	active bool
+}
+
+type testImage struct {
+	name   string
+	target ocispec.Descriptor
+}
+
+type testContainer struct {
+	id       string
+	snapshot string
+}
+
+func newStores(t testing.TB) (*DB, content.Store, snapshot.Snapshotter, func()) {
+	td, err := ioutil.TempDir("", "gc-test-")
+	if err != nil {
+		t.Fatal(err)
+	}
+	db, err := bolt.Open(filepath.Join(td, "meta.db"), 0644, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	nsn, err := naive.NewSnapshotter(filepath.Join(td, "snapshots"))
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	lcs, err := local.NewStore(filepath.Join(td, "content"))
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	mdb := NewDB(db, lcs, map[string]snapshot.Snapshotter{"naive": nsn})
+
+	return mdb, mdb.ContentStore(), mdb.Snapshotter("naive"), func() {
+		os.RemoveAll(td)
+	}
+}
diff --git a/metadata/gc.go b/metadata/gc.go
new file mode 100644
index 000000000..8434d694b
--- /dev/null
+++ b/metadata/gc.go
@@ -0,0 +1,343 @@
+package metadata
+
+import (
+	"context"
+	"fmt"
+	"strings"
+
+	"github.com/boltdb/bolt"
+	"github.com/containerd/containerd/gc"
+	"github.com/containerd/containerd/log"
+	"github.com/pkg/errors"
+)
+
+const (
+	ResourceUnknown gc.ResourceType = iota
+	ResourceContent
+	ResourceSnapshot
+	ResourceContainer
+	ResourceTask
+)
+
+var (
+	labelGCRoot       = []byte("containerd.io/gc.root")
+	labelGCSnapRef    = []byte("containerd.io/gc.ref.snapshot.")
+	labelGCContentRef = []byte("containerd.io/gc.ref.content")
+)
+
+func scanRoots(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+	v1bkt := tx.Bucket(bucketKeyVersion)
+	if v1bkt == nil {
+		return nil
+	}
+
+	// iterate through each namespace
+	v1c := v1bkt.Cursor()
+
+	for k, v := v1c.First(); k != nil; k, v = v1c.Next() {
+		if v != nil {
+			continue
+		}
+		nbkt := v1bkt.Bucket(k)
+		ns := string(k)
+
+		ibkt := nbkt.Bucket(bucketKeyObjectImages)
+		if ibkt != nil {
+			if err := ibkt.ForEach(func(k, v []byte) error {
+				if v != nil {
+					return nil
+				}
+
+				target := ibkt.Bucket(k).Bucket(bucketKeyTarget)
+				if target != nil {
+					contentKey := string(target.Get(bucketKeyDigest))
+					select {
+					case nc <- gcnode(ResourceContent, ns, contentKey):
+					case <-ctx.Done():
+						return ctx.Err()
+					}
+				}
+				return sendSnapshotRefs(ns, ibkt.Bucket(k), func(n gc.Node) {
+					select {
+					case nc <- n:
+					case <-ctx.Done():
+					}
+				})
+			}); err != nil {
+				return err
+			}
+		}
+
+		cbkt := nbkt.Bucket(bucketKeyObjectContent)
+		if cbkt != nil {
+			cbkt = cbkt.Bucket(bucketKeyObjectBlob)
+		}
+		if cbkt != nil {
+			if err := cbkt.ForEach(func(k, v []byte) error {
+				if v != nil {
+					return nil
+				}
+				return sendRootRef(ctx, nc, gcnode(ResourceContent, ns, string(k)), cbkt.Bucket(k))
+			}); err != nil {
+				return err
+			}
+		}
+
+		cbkt = nbkt.Bucket(bucketKeyObjectContainers)
+		if cbkt != nil {
+			if err := cbkt.ForEach(func(k, v []byte) error {
+				if v != nil {
+					return nil
+				}
+				snapshotter := string(cbkt.Bucket(k).Get(bucketKeySnapshotter))
+				if snapshotter != "" {
+					ss := string(cbkt.Bucket(k).Get(bucketKeySnapshotKey))
+					select {
+					case nc <- gcnode(ResourceSnapshot, ns, fmt.Sprintf("%s/%s", snapshotter, ss)):
+					case <-ctx.Done():
+						return ctx.Err()
+					}
+				}
+
+				// TODO: Send additional snapshot refs through labels
+				return sendSnapshotRefs(ns, cbkt.Bucket(k), func(n gc.Node) {
+					select {
+					case nc <- n:
+					case <-ctx.Done():
+					}
+				})
+			}); err != nil {
+				return err
+			}
+		}
+
+		sbkt := nbkt.Bucket(bucketKeyObjectSnapshots)
+		if sbkt != nil {
+			if err := sbkt.ForEach(func(sk, sv []byte) error {
+				if sv != nil {
+					return nil
+				}
+				snbkt := sbkt.Bucket(sk)
+
+				return snbkt.ForEach(func(k, v []byte) error {
+					if v != nil {
+						return nil
+					}
+
+					return sendRootRef(ctx, nc, gcnode(ResourceSnapshot, ns, fmt.Sprintf("%s/%s", sk, k)), snbkt.Bucket(k))
+				})
+			}); err != nil {
+				return err
+			}
+		}
+	}
+	return nil
+}
+
+func references(ctx context.Context, tx *bolt.Tx, node gc.Node, fn func(gc.Node)) error {
+	if node.Type == ResourceContent {
+		bkt := getBucket(tx, bucketKeyVersion, []byte(node.Namespace), bucketKeyObjectContent, bucketKeyObjectBlob, []byte(node.Key))
+		if bkt == nil {
+			// Node may be created from dead edge
+			return nil
+		}
+
+		if err := sendSnapshotRefs(node.Namespace, bkt, fn); err != nil {
+			return err
+		}
+		return sendContentRefs(node.Namespace, bkt, fn)
+	} else if node.Type == ResourceSnapshot {
+		parts := strings.SplitN(node.Key, "/", 2)
+		if len(parts) != 2 {
+			return errors.Errorf("invalid snapshot gc key %s", node.Key)
+		}
+		ss := parts[0]
+		name := parts[1]
+
+		bkt := getBucket(tx, bucketKeyVersion, []byte(node.Namespace), bucketKeyObjectSnapshots, []byte(ss), []byte(name))
+		if bkt == nil {
+			getBucket(tx, bucketKeyVersion, []byte(node.Namespace), bucketKeyObjectSnapshots).ForEach(func(k, v []byte) error {
+				return nil
+			})
+
+			// Node may be created from dead edge
+			return nil
+		}
+
+		if pv := bkt.Get(bucketKeyParent); len(pv) > 0 {
+			fn(gcnode(ResourceSnapshot, node.Namespace, fmt.Sprintf("%s/%s", ss, pv)))
+		}
+
+		return sendSnapshotRefs(node.Namespace, bkt, fn)
+	}
+
+	return nil
+}
+
+func scanAll(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+	v1bkt := tx.Bucket(bucketKeyVersion)
+	if v1bkt == nil {
+		return nil
+	}
+
+	// iterate through each namespace
+	v1c := v1bkt.Cursor()
+
+	for k, v := v1c.First(); k != nil; k, v = v1c.Next() {
+		if v != nil {
+			continue
+		}
+		nbkt := v1bkt.Bucket(k)
+		ns := string(k)
+
+		sbkt := nbkt.Bucket(bucketKeyObjectSnapshots)
+		if sbkt != nil {
+			if err := sbkt.ForEach(func(sk, sv []byte) error {
+				if sv != nil {
+					return nil
+				}
+				snbkt := sbkt.Bucket(sk)
+				return snbkt.ForEach(func(k, v []byte) error {
+					if v != nil {
+						return nil
+					}
+					select {
+					case nc <- gcnode(ResourceSnapshot, ns, fmt.Sprintf("%s/%s", sk, k)):
+					case <-ctx.Done():
+						return ctx.Err()
+					}
+					return nil
+				})
+			}); err != nil {
+				return err
+			}
+		}
+
+		cbkt := nbkt.Bucket(bucketKeyObjectContent)
+		if cbkt != nil {
+			cbkt = cbkt.Bucket(bucketKeyObjectBlob)
+		}
+		if cbkt != nil {
+			if err := cbkt.ForEach(func(k, v []byte) error {
+				if v != nil {
+					return nil
+				}
+				select {
+				case nc <- gcnode(ResourceContent, ns, string(k)):
+				case <-ctx.Done():
+					return ctx.Err()
+				}
+				return nil
+			}); err != nil {
+				return err
+			}
+		}
+	}
+
+	return nil
+}
+
+func remove(ctx context.Context, tx *bolt.Tx, node gc.Node) error {
+	v1bkt := tx.Bucket(bucketKeyVersion)
+	if v1bkt == nil {
+		return nil
+	}
+
+	nsbkt := v1bkt.Bucket([]byte(node.Namespace))
+	if nsbkt == nil {
+		return nil
+	}
+
+	switch node.Type {
+	case ResourceContent:
+		cbkt := nsbkt.Bucket(bucketKeyObjectContent)
+		if cbkt != nil {
+			cbkt = cbkt.Bucket(bucketKeyObjectBlob)
+		}
+		if cbkt != nil {
+			log.G(ctx).WithField("key", node.Key).Debug("delete content")
+			return cbkt.DeleteBucket([]byte(node.Key))
+		}
+	case ResourceSnapshot:
+		sbkt := nsbkt.Bucket(bucketKeyObjectSnapshots)
+		if sbkt != nil {
+			parts := strings.SplitN(node.Key, "/", 2)
+			if len(parts) != 2 {
+				return errors.Errorf("invalid snapshot gc key %s", node.Key)
+			}
+			ssbkt := sbkt.Bucket([]byte(parts[0]))
+			if ssbkt != nil {
+				log.G(ctx).WithField("key", parts[1]).WithField("snapshotter", parts[0]).Debug("delete snapshot")
+				return ssbkt.DeleteBucket([]byte(parts[1]))
+			}
+		}
+	}
+
+	return nil
+}
+
+// sendSnapshotRefs sends all snapshot references referred to by the labels in the bkt
+func sendSnapshotRefs(ns string, bkt *bolt.Bucket, fn func(gc.Node)) error {
+	lbkt := bkt.Bucket(bucketKeyObjectLabels)
+	if lbkt != nil {
+		lc := lbkt.Cursor()
+
+		for k, v := lc.Seek(labelGCSnapRef); k != nil && strings.HasPrefix(string(k), string(labelGCSnapRef)); k, v = lc.Next() {
+			snapshotter := string(k[len(labelGCSnapRef):])
+			fn(gcnode(ResourceSnapshot, ns, fmt.Sprintf("%s/%s", snapshotter, v)))
+		}
+	}
+	return nil
+}
+
+// sendContentRefs sends all content references referred to by the labels in the bkt
+func sendContentRefs(ns string, bkt *bolt.Bucket, fn func(gc.Node)) error {
+	lbkt := bkt.Bucket(bucketKeyObjectLabels)
+	if lbkt != nil {
+		lc := lbkt.Cursor()
+
+		labelRef := string(labelGCContentRef)
+		for k, v := lc.Seek(labelGCContentRef); k != nil && strings.HasPrefix(string(k), labelRef); k, v = lc.Next() {
+			if ks := string(k); ks != labelRef {
+				// Allow reference naming, ignore names
+				if ks[len(labelRef)] != '.' {
+					continue
+				}
+			}
+
+			fn(gcnode(ResourceContent, ns, string(v)))
+		}
+	}
+	return nil
+}
+
+func isRootRef(bkt *bolt.Bucket) bool {
+	lbkt := bkt.Bucket(bucketKeyObjectLabels)
+	if lbkt != nil {
+		rv := lbkt.Get(labelGCRoot)
+		if rv != nil {
+			// TODO: interpret rv as a timestamp and skip if expired
+			return true
+		}
+	}
+	return false
+}
+
+func sendRootRef(ctx context.Context, nc chan<- gc.Node, n gc.Node, bkt *bolt.Bucket) error {
+	if isRootRef(bkt) {
+		select {
+		case nc <- n:
+		case <-ctx.Done():
+			return ctx.Err()
+		}
+	}
+	return nil
+}
+
+func gcnode(t gc.ResourceType, ns, key string) gc.Node {
+	return gc.Node{
+		Type:      t,
+		Namespace: ns,
+		Key:       key,
+	}
+}
diff --git a/metadata/gc_test.go b/metadata/gc_test.go
new file mode 100644
index 000000000..78422cd81
--- /dev/null
+++ b/metadata/gc_test.go
@@ -0,0 +1,406 @@
+package metadata
+
+import (
+	"context"
+	"io"
+	"io/ioutil"
+	"math/rand"
+	"os"
+	"path/filepath"
+	"sort"
+	"testing"
+
+	"github.com/boltdb/bolt"
+	"github.com/containerd/containerd/gc"
+	"github.com/containerd/containerd/metadata/boltutil"
+	digest "github.com/opencontainers/go-digest"
+)
+
+func TestGCRoots(t *testing.T) {
+	db, cleanup, err := newDatabase()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer cleanup()
+
+	alters := []alterFunc{
+		addImage("ns1", "image1", dgst(1), nil),
+		addImage("ns1", "image2", dgst(2), labelmap(string(labelGCSnapRef)+"overlay", "sn2")),
+		addContent("ns1", dgst(1), nil),
+		addContent("ns1", dgst(2), nil),
+		addContent("ns1", dgst(3), nil),
+		addContent("ns2", dgst(1), nil),
+		addContent("ns2", dgst(2), labelmap(string(labelGCRoot), "always")),
+		addSnapshot("ns1", "overlay", "sn1", "", nil),
+		addSnapshot("ns1", "overlay", "sn2", "", nil),
+		addSnapshot("ns1", "overlay", "sn3", "", labelmap(string(labelGCRoot), "always")),
+	}
+
+	expected := []gc.Node{
+		gcnode(ResourceContent, "ns1", dgst(1).String()),
+		gcnode(ResourceContent, "ns1", dgst(2).String()),
+		gcnode(ResourceContent, "ns2", dgst(2).String()),
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn2"),
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn3"),
+	}
+
+	if err := db.Update(func(tx *bolt.Tx) error {
+		v1bkt, err := tx.CreateBucketIfNotExists(bucketKeyVersion)
+		if err != nil {
+			return err
+		}
+		for _, alter := range alters {
+			if err := alter(v1bkt); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		t.Fatalf("Update failed: %+v", err)
+	}
+
+	ctx := context.Background()
+
+	checkNodes(ctx, t, db, expected, func(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+		return scanRoots(ctx, tx, nc)
+	})
+}
+
+func TestGCRemove(t *testing.T) {
+	db, cleanup, err := newDatabase()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer cleanup()
+
+	alters := []alterFunc{
+		addImage("ns1", "image1", dgst(1), nil),
+		addImage("ns1", "image2", dgst(2), labelmap(string(labelGCSnapRef)+"overlay", "sn2")),
+		addContent("ns1", dgst(1), nil),
+		addContent("ns1", dgst(2), nil),
+		addContent("ns1", dgst(3), nil),
+		addContent("ns2", dgst(1), nil),
+		addContent("ns2", dgst(2), labelmap(string(labelGCRoot), "always")),
+		addSnapshot("ns1", "overlay", "sn1", "", nil),
+		addSnapshot("ns1", "overlay", "sn2", "", nil),
+		addSnapshot("ns1", "overlay", "sn3", "", labelmap(string(labelGCRoot), "always")),
+		addSnapshot("ns2", "overlay", "sn1", "", nil),
+	}
+
+	all := []gc.Node{
+		gcnode(ResourceContent, "ns1", dgst(1).String()),
+		gcnode(ResourceContent, "ns1", dgst(2).String()),
+		gcnode(ResourceContent, "ns1", dgst(3).String()),
+		gcnode(ResourceContent, "ns2", dgst(1).String()),
+		gcnode(ResourceContent, "ns2", dgst(2).String()),
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn1"),
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn2"),
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn3"),
+		gcnode(ResourceSnapshot, "ns2", "overlay/sn1"),
+	}
+
+	var deleted, remaining []gc.Node
+	for i, n := range all {
+		if i%2 == 0 {
+			deleted = append(deleted, n)
+		} else {
+			remaining = append(remaining, n)
+		}
+	}
+
+	if err := db.Update(func(tx *bolt.Tx) error {
+		v1bkt, err := tx.CreateBucketIfNotExists(bucketKeyVersion)
+		if err != nil {
+			return err
+		}
+		for _, alter := range alters {
+			if err := alter(v1bkt); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		t.Fatalf("Update failed: %+v", err)
+	}
+
+	ctx := context.Background()
+
+	checkNodes(ctx, t, db, all, func(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+		return scanAll(ctx, tx, nc)
+	})
+	if t.Failed() {
+		t.Fatal("Scan all failed")
+	}
+
+	if err := db.Update(func(tx *bolt.Tx) error {
+		for _, n := range deleted {
+			if err := remove(ctx, tx, n); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		t.Fatalf("Update failed: %+v", err)
+	}
+
+	checkNodes(ctx, t, db, remaining, func(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+		return scanAll(ctx, tx, nc)
+	})
+}
+
+func TestGCRefs(t *testing.T) {
+	db, cleanup, err := newDatabase()
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer cleanup()
+
+	alters := []alterFunc{
+		addContent("ns1", dgst(1), nil),
+		addContent("ns1", dgst(2), nil),
+		addContent("ns1", dgst(3), nil),
+		addContent("ns1", dgst(4), labelmap(string(labelGCContentRef), dgst(1).String())),
+		addContent("ns1", dgst(5), labelmap(string(labelGCContentRef)+".anything-1", dgst(2).String(), string(labelGCContentRef)+".anything-2", dgst(3).String())),
+		addContent("ns1", dgst(6), labelmap(string(labelGCContentRef)+"bad", dgst(1).String())),
+		addContent("ns2", dgst(1), nil),
+		addContent("ns2", dgst(2), nil),
+		addSnapshot("ns1", "overlay", "sn1", "", nil),
+		addSnapshot("ns1", "overlay", "sn2", "sn1", nil),
+		addSnapshot("ns1", "overlay", "sn3", "sn2", nil),
+		addSnapshot("ns1", "overlay", "sn4", "", labelmap(string(labelGCSnapRef)+"btrfs", "sn1", string(labelGCSnapRef)+"overlay", "sn1")),
+		addSnapshot("ns1", "btrfs", "sn1", "", nil),
+		addSnapshot("ns2", "overlay", "sn1", "", nil),
+		addSnapshot("ns2", "overlay", "sn2", "sn1", nil),
+	}
+
+	refs := map[gc.Node][]gc.Node{
+		gcnode(ResourceContent, "ns1", dgst(1).String()): nil,
+		gcnode(ResourceContent, "ns1", dgst(2).String()): nil,
+		gcnode(ResourceContent, "ns1", dgst(3).String()): nil,
+		gcnode(ResourceContent, "ns1", dgst(4).String()): {
+			gcnode(ResourceContent, "ns1", dgst(1).String()),
+		},
+		gcnode(ResourceContent, "ns1", dgst(5).String()): {
+			gcnode(ResourceContent, "ns1", dgst(2).String()),
+			gcnode(ResourceContent, "ns1", dgst(3).String()),
+		},
+		gcnode(ResourceContent, "ns1", dgst(6).String()): nil,
+		gcnode(ResourceContent, "ns2", dgst(1).String()): nil,
+		gcnode(ResourceContent, "ns2", dgst(2).String()): nil,
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn1"):   nil,
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn2"): {
+			gcnode(ResourceSnapshot, "ns1", "overlay/sn1"),
+		},
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn3"): {
+			gcnode(ResourceSnapshot, "ns1", "overlay/sn2"),
+		},
+		gcnode(ResourceSnapshot, "ns1", "overlay/sn4"): {
+			gcnode(ResourceSnapshot, "ns1", "btrfs/sn1"),
+			gcnode(ResourceSnapshot, "ns1", "overlay/sn1"),
+		},
+		gcnode(ResourceSnapshot, "ns1", "btrfs/sn1"):   nil,
+		gcnode(ResourceSnapshot, "ns2", "overlay/sn1"): nil,
+		gcnode(ResourceSnapshot, "ns2", "overlay/sn2"): {
+			gcnode(ResourceSnapshot, "ns2", "overlay/sn1"),
+		},
+	}
+
+	if err := db.Update(func(tx *bolt.Tx) error {
+		v1bkt, err := tx.CreateBucketIfNotExists(bucketKeyVersion)
+		if err != nil {
+			return err
+		}
+		for _, alter := range alters {
+			if err := alter(v1bkt); err != nil {
+				return err
+			}
+		}
+		return nil
+	}); err != nil {
+		t.Fatalf("Update failed: %+v", err)
+	}
+
+	ctx := context.Background()
+
+	for n, nodes := range refs {
+		checkNodes(ctx, t, db, nodes, func(ctx context.Context, tx *bolt.Tx, nc chan<- gc.Node) error {
+			return references(ctx, tx, n, func(n gc.Node) {
+				select {
+				case nc <- n:
+				case <-ctx.Done():
+				}
+			})
+		})
+		if t.Failed() {
+			t.Fatalf("Failure scanning %v", n)
+		}
+	}
+}
+
+func newDatabase() (*bolt.DB, func(), error) {
+	td, err := ioutil.TempDir("", "gc-roots-")
+	if err != nil {
+		return nil, nil, err
+	}
+
+	db, err := bolt.Open(filepath.Join(td, "test.db"), 0777, nil)
+	if err != nil {
+		os.RemoveAll(td)
+		return nil, nil, err
+	}
+
+	return db, func() {
+		db.Close()
+		os.RemoveAll(td)
+	}, nil
+}
+
+func checkNodes(ctx context.Context, t *testing.T, db *bolt.DB, expected []gc.Node, fn func(context.Context, *bolt.Tx, chan<- gc.Node) error) {
+	var actual []gc.Node
+	nc := make(chan gc.Node)
+	done := make(chan struct{})
+	go func() {
+		defer close(done)
+		for n := range nc {
+			actual = append(actual, n)
+		}
+	}()
+	if err := db.View(func(tx *bolt.Tx) error {
+		defer close(nc)
+		return fn(ctx, tx, nc)
+	}); err != nil {
+		t.Fatal(err)
+	}
+
+	<-done
+	checkNodesEqual(t, actual, expected)
+}
+
+func checkNodesEqual(t *testing.T, n1, n2 []gc.Node) {
+	sort.Sort(nodeList(n1))
+	sort.Sort(nodeList(n2))
+
+	if len(n1) != len(n2) {
+		t.Errorf("Nodes do not match\n\tExpected:\n\t%v\n\tActual:\n\t%v", n2, n1)
+		return
+	}
+
+	for i := range n1 {
+		if n1[i] != n2[i] {
+			t.Errorf("[%d] root does not match expected: expected %v, got %v", i, n2[i], n1[i])
+		}
+	}
+}
+
+type nodeList []gc.Node
+
+func (nodes nodeList) Len() int {
+	return len(nodes)
+}
+
+func (nodes nodeList) Less(i, j int) bool {
+	if nodes[i].Type != nodes[j].Type {
+		return nodes[i].Type < nodes[j].Type
+	}
+	if nodes[i].Namespace != nodes[j].Namespace {
+		return nodes[i].Namespace < nodes[j].Namespace
+	}
+	return nodes[i].Key < nodes[j].Key
+}
+
+func (nodes nodeList) Swap(i, j int) {
+	nodes[i], nodes[j] = nodes[j], nodes[i]
+}
+
+type alterFunc func(bkt *bolt.Bucket) error
+
+func addImage(ns, name string, dgst digest.Digest, labels map[string]string) alterFunc {
+	return func(bkt *bolt.Bucket) error {
+		ibkt, err := createBuckets(bkt, ns, string(bucketKeyObjectImages), name)
+		if err != nil {
+			return err
+		}
+
+		tbkt, err := ibkt.CreateBucket(bucketKeyTarget)
+		if err != nil {
+			return err
+		}
+		if err := tbkt.Put(bucketKeyDigest, []byte(dgst.String())); err != nil {
+			return err
+		}
+
+		return boltutil.WriteLabels(ibkt, labels)
+	}
+}
+
+func addSnapshot(ns, snapshotter, name, parent string, labels map[string]string) alterFunc {
+	return func(bkt *bolt.Bucket) error {
+		sbkt, err := createBuckets(bkt, ns, string(bucketKeyObjectSnapshots), snapshotter, name)
+		if err != nil {
+			return err
+		}
+		if parent != "" {
+			if err := sbkt.Put(bucketKeyParent, []byte(parent)); err != nil {
+				return err
+			}
+		}
+		return boltutil.WriteLabels(sbkt, labels)
+	}
+}
+
+func addContent(ns string, dgst digest.Digest, labels map[string]string) alterFunc {
+	return func(bkt *bolt.Bucket) error {
+		cbkt, err := createBuckets(bkt, ns, string(bucketKeyObjectContent), string(bucketKeyObjectBlob), dgst.String())
+		if err != nil {
+			return err
+		}
+		return boltutil.WriteLabels(cbkt, labels)
+	}
+}
+
+func addContainer(ns, name, snapshotter, snapshot string, labels map[string]string) alterFunc {
+	return func(bkt *bolt.Bucket) error {
+		cbkt, err := createBuckets(bkt, ns, string(bucketKeyObjectContainers), name)
+		if err != nil {
+			return err
+		}
+		if err := cbkt.Put(bucketKeySnapshotter, []byte(snapshotter)); err != nil {
+			return err
+		}
+		if err := cbkt.Put(bucketKeySnapshotKey, []byte(snapshot)); err != nil {
+			return err
+		}
+		return boltutil.WriteLabels(cbkt, labels)
+	}
+}
+
+func createBuckets(bkt *bolt.Bucket, names ...string) (*bolt.Bucket, error) {
+	for _, name := range names {
+		nbkt, err := bkt.CreateBucketIfNotExists([]byte(name))
+		if err != nil {
+			return nil, err
+		}
+		bkt = nbkt
+	}
+	return bkt, nil
+}
+
+func labelmap(kv ...string) map[string]string {
+	if len(kv)%2 != 0 {
+		panic("bad labels argument")
+	}
+	l := map[string]string{}
+	for i := 0; i < len(kv); i = i + 2 {
+		l[kv[i]] = kv[i+1]
+	}
+	return l
+}
+
+func dgst(i int64) digest.Digest {
+	r := rand.New(rand.NewSource(i))
+	dgstr := digest.SHA256.Digester()
+	if _, err := io.CopyN(dgstr.Hash(), r, 256); err != nil {
+		panic(err)
+	}
+	return dgstr.Digest()
+}
diff --git a/metadata/snapshot.go b/metadata/snapshot.go
index 4103827a4..ad38e5915 100644
--- a/metadata/snapshot.go
+++ b/metadata/snapshot.go
@@ -4,11 +4,13 @@ import (
 	"context"
 	"fmt"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/boltdb/bolt"
 	"github.com/containerd/containerd/errdefs"
 	"github.com/containerd/containerd/labels"
+	"github.com/containerd/containerd/log"
 	"github.com/containerd/containerd/metadata/boltutil"
 	"github.com/containerd/containerd/mount"
 	"github.com/containerd/containerd/namespaces"
@@ -19,12 +21,13 @@ import (
 type snapshotter struct {
 	snapshot.Snapshotter
 	name string
-	db   transactor
+	db   *DB
+	l    sync.RWMutex
 }
 
 // newSnapshotter returns a new Snapshotter which namespaces the given snapshot
 // using the provided name and database.
-func newSnapshotter(db transactor, name string, sn snapshot.Snapshotter) snapshot.Snapshotter {
+func newSnapshotter(db *DB, name string, sn snapshot.Snapshotter) *snapshotter {
 	return &snapshotter{
 		Snapshotter: sn,
 		name:        name,
@@ -125,6 +128,9 @@ func (s *snapshotter) Stat(ctx context.Context, key string) (snapshot.Info, erro
 }
 
 func (s *snapshotter) Update(ctx context.Context, info snapshot.Info, fieldpaths ...string) (snapshot.Info, error) {
+	s.l.RLock()
+	defer s.l.RUnlock()
+
 	ns, err := namespaces.NamespaceRequired(ctx)
 	if err != nil {
 		return snapshot.Info{}, err
@@ -249,6 +255,9 @@ func (s *snapshotter) View(ctx context.Context, key, parent string, opts ...snap
 }
 
 func (s *snapshotter) createSnapshot(ctx context.Context, key, parent string, readonly bool, opts []snapshot.Opt) ([]mount.Mount, error) {
+	s.l.RLock()
+	defer s.l.RUnlock()
+
 	ns, err := namespaces.NamespaceRequired(ctx)
 	if err != nil {
 		return nil, err
@@ -332,6 +341,9 @@ func (s *snapshotter) createSnapshot(ctx context.Context, key, parent string, re
 }
 
 func (s *snapshotter) Commit(ctx context.Context, name, key string, opts ...snapshot.Opt) error {
+	s.l.RLock()
+	defer s.l.RUnlock()
+
 	ns, err := namespaces.NamespaceRequired(ctx)
 	if err != nil {
 		return err
@@ -421,6 +433,9 @@ func (s *snapshotter) Commit(ctx context.Context, name, key string, opts ...snap
 }
 
 func (s *snapshotter) Remove(ctx context.Context, key string) error {
+	s.l.RLock()
+	defer s.l.RUnlock()
+
 	ns, err := namespaces.NamespaceRequired(ctx)
 	if err != nil {
 		return err
@@ -457,7 +472,16 @@ func (s *snapshotter) Remove(ctx context.Context, key string) error {
 			}
 		}
 
-		return bkt.DeleteBucket([]byte(key))
+		if err := bkt.DeleteBucket([]byte(key)); err != nil {
+			return err
+		}
+
+		// Mark snapshotter as dirty for triggering garbage collection
+		s.db.dirtyL.Lock()
+		s.db.dirtySS[s.name] = struct{}{}
+		s.db.dirtyL.Unlock()
+
+		return nil
 	})
 }
 
@@ -565,3 +589,134 @@ func validateSnapshot(info *snapshot.Info) error {
 
 	return nil
 }
+
+func (s *snapshotter) garbageCollect(ctx context.Context) error {
+	logger := log.G(ctx).WithField("snapshotter", s.name)
+	lt1 := time.Now()
+	s.l.Lock()
+	defer func() {
+		s.l.Unlock()
+		logger.WithField("t", time.Now().Sub(lt1)).Debugf("garbage collected")
+	}()
+
+	seen := map[string]struct{}{}
+	if err := s.db.View(func(tx *bolt.Tx) error {
+		v1bkt := tx.Bucket(bucketKeyVersion)
+		if v1bkt == nil {
+			return nil
+		}
+
+		// iterate through each namespace
+		v1c := v1bkt.Cursor()
+
+		for k, v := v1c.First(); k != nil; k, v = v1c.Next() {
+			if v != nil {
+				continue
+			}
+
+			sbkt := v1bkt.Bucket(k).Bucket(bucketKeyObjectSnapshots)
+			if sbkt == nil {
+				continue
+			}
+
+			// Load specific snapshotter
+			ssbkt := sbkt.Bucket([]byte(s.name))
+			if ssbkt == nil {
+				continue
+			}
+
+			if err := ssbkt.ForEach(func(sk, sv []byte) error {
+				if sv == nil {
+					bkey := ssbkt.Bucket(sk).Get(bucketKeyName)
+					if len(bkey) > 0 {
+						seen[string(bkey)] = struct{}{}
+					}
+				}
+				return nil
+			}); err != nil {
+				return err
+			}
+		}
+
+		return nil
+	}); err != nil {
+		return err
+	}
+
+	roots, err := s.walkTree(ctx, seen)
+	if err != nil {
+		return err
+	}
+
+	// TODO: Unlock before prune (once nodes are fully unavailable)
+
+	for _, node := range roots {
+		if err := s.pruneBranch(ctx, node); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+type treeNode struct {
+	info     snapshot.Info
+	remove   bool
+	children []*treeNode
+}
+
+func (s *snapshotter) walkTree(ctx context.Context, seen map[string]struct{}) ([]*treeNode, error) {
+	roots := []*treeNode{}
+	nodes := map[string]*treeNode{}
+
+	if err := s.Snapshotter.Walk(ctx, func(ctx context.Context, info snapshot.Info) error {
+		_, isSeen := seen[info.Name]
+		node, ok := nodes[info.Name]
+		if !ok {
+			node = &treeNode{}
+			nodes[info.Name] = node
+		}
+
+		node.remove = !isSeen
+		node.info = info
+
+		if info.Parent == "" {
+			roots = append(roots, node)
+		} else {
+			parent, ok := nodes[info.Parent]
+			if !ok {
+				parent = &treeNode{}
+				nodes[info.Parent] = parent
+			}
+			parent.children = append(parent.children, node)
+		}
+
+		return nil
+	}); err != nil {
+		return nil, err
+	}
+
+	return roots, nil
+}
+
+func (s *snapshotter) pruneBranch(ctx context.Context, node *treeNode) error {
+	for _, child := range node.children {
+		if err := s.pruneBranch(ctx, child); err != nil {
+			return err
+		}
+	}
+
+	if node.remove {
+		logger := log.G(ctx).WithField("snapshotter", s.name)
+		if err := s.Snapshotter.Remove(ctx, node.info.Name); err != nil {
+			if !errdefs.IsFailedPrecondition(err) {
+				return err
+			}
+			logger.WithError(err).WithField("key", node.info.Name).Warnf("snapshot removal failed")
+		} else {
+			logger.WithField("key", node.info.Name).Debug("removed snapshot")
+		}
+	}
+
+	return nil
+}
diff --git a/remotes/handlers.go b/remotes/handlers.go
index 0a4db6bce..f92bb469d 100644
--- a/remotes/handlers.go
+++ b/remotes/handlers.go
@@ -2,6 +2,7 @@ package remotes
 
 import (
 	"context"
+	"encoding/json"
 	"fmt"
 	"io"
 	"time"
@@ -11,6 +12,7 @@ import (
 	"github.com/containerd/containerd/images"
 	"github.com/containerd/containerd/log"
 	ocispec "github.com/opencontainers/image-spec/specs-go/v1"
+	"github.com/pkg/errors"
 	"github.com/sirupsen/logrus"
 )
 
@@ -102,7 +104,76 @@ func fetch(ctx context.Context, ingester content.Ingester, fetcher Fetcher, desc
 	}
 	defer rc.Close()
 
-	return content.Copy(ctx, cw, rc, desc.Size, desc.Digest)
+	r, opts := commitOpts(desc, rc)
+	return content.Copy(ctx, cw, r, desc.Size, desc.Digest, opts...)
+}
+
+// commitOpts gets the appropriate content options to alter
+// the content info on commit based on media type.
+func commitOpts(desc ocispec.Descriptor, r io.Reader) (io.Reader, []content.Opt) {
+	var childrenF func(r io.Reader) ([]ocispec.Descriptor, error)
+
+	switch desc.MediaType {
+	case images.MediaTypeDockerSchema2Manifest, ocispec.MediaTypeImageManifest:
+		childrenF = func(r io.Reader) ([]ocispec.Descriptor, error) {
+			var (
+				manifest ocispec.Manifest
+				decoder  = json.NewDecoder(r)
+			)
+			if err := decoder.Decode(&manifest); err != nil {
+				return nil, err
+			}
+
+			return append([]ocispec.Descriptor{manifest.Config}, manifest.Layers...), nil
+		}
+	case images.MediaTypeDockerSchema2ManifestList, ocispec.MediaTypeImageIndex:
+		childrenF = func(r io.Reader) ([]ocispec.Descriptor, error) {
+			var (
+				index   ocispec.Index
+				decoder = json.NewDecoder(r)
+			)
+			if err := decoder.Decode(&index); err != nil {
+				return nil, err
+			}
+
+			return index.Manifests, nil
+		}
+	default:
+		return r, nil
+	}
+
+	pr, pw := io.Pipe()
+
+	var children []ocispec.Descriptor
+	errC := make(chan error)
+
+	go func() {
+		defer close(errC)
+		ch, err := childrenF(pr)
+		if err != nil {
+			errC <- err
+		}
+		children = ch
+	}()
+
+	opt := func(info *content.Info) error {
+		err := <-errC
+		if err != nil {
+			return errors.Wrap(err, "unable to get commit labels")
+		}
+
+		if len(children) > 0 {
+			if info.Labels == nil {
+				info.Labels = map[string]string{}
+			}
+			for i, ch := range children {
+				info.Labels[fmt.Sprintf("containerd.io/gc.ref.content.%d", i)] = ch.Digest.String()
+			}
+		}
+		return nil
+	}
+
+	return io.TeeReader(r, pw), []content.Opt{opt}
 }
 
 // PushHandler returns a handler that will push all content from the provider
diff --git a/rootfs/apply.go b/rootfs/apply.go
index 4e21fd10f..a198c99f9 100644
--- a/rootfs/apply.go
+++ b/rootfs/apply.go
@@ -63,8 +63,8 @@ func ApplyLayer(ctx context.Context, layer Layer, chain []digest.Digest, sn snap
 
 	key := fmt.Sprintf("extract-%s %s", uniquePart(), chainID)
 
-	// Prepare snapshot with from parent
-	mounts, err := sn.Prepare(ctx, key, parent.String())
+	// Prepare snapshot with from parent, label as root
+	mounts, err := sn.Prepare(ctx, key, parent.String(), opts...)
 	if err != nil {
 		//TODO: If is snapshot exists error, retry
 		return false, errors.Wrap(err, "failed to prepare extraction layer")
@@ -87,7 +87,7 @@ func ApplyLayer(ctx context.Context, layer Layer, chain []digest.Digest, sn snap
 		return false, err
 	}
 
-	if err = sn.Commit(ctx, chainID.String(), key); err != nil {
+	if err = sn.Commit(ctx, chainID.String(), key, opts...); err != nil {
 		if !errdefs.IsAlreadyExists(err) {
 			return false, errors.Wrapf(err, "failed to commit snapshot %s", parent)
 		}
diff --git a/services/containers/service.go b/services/containers/service.go
index 428de476d..c5322f874 100644
--- a/services/containers/service.go
+++ b/services/containers/service.go
@@ -10,6 +10,7 @@ import (
 	"github.com/containerd/containerd/metadata"
 	"github.com/containerd/containerd/plugin"
 	"github.com/golang/protobuf/ptypes/empty"
+	"github.com/pkg/errors"
 	"golang.org/x/net/context"
 	"google.golang.org/grpc"
 	"google.golang.org/grpc/codes"
@@ -160,6 +161,10 @@ func (s *Service) Delete(ctx context.Context, req *api.DeleteContainerRequest) (
 		return &empty.Empty{}, err
 	}
 
+	if err := s.db.GarbageCollect(ctx); err != nil {
+		return &empty.Empty{}, errdefs.ToGRPC(errors.Wrap(err, "garbage collection failed"))
+	}
+
 	return &empty.Empty{}, nil
 }
 
diff --git a/services/images/service.go b/services/images/service.go
index 6c5d3b685..fa8a00aae 100644
--- a/services/images/service.go
+++ b/services/images/service.go
@@ -10,6 +10,7 @@ import (
 	"github.com/containerd/containerd/metadata"
 	"github.com/containerd/containerd/plugin"
 	"github.com/golang/protobuf/ptypes/empty"
+	"github.com/pkg/errors"
 	"golang.org/x/net/context"
 	"google.golang.org/grpc"
 	"google.golang.org/grpc/codes"
@@ -161,6 +162,10 @@ func (s *Service) Delete(ctx context.Context, req *imagesapi.DeleteImageRequest)
 		return nil, err
 	}
 
+	if err := s.db.GarbageCollect(ctx); err != nil {
+		return nil, errdefs.ToGRPC(errors.Wrap(err, "garbage collection failed"))
+	}
+
 	return &empty.Empty{}, nil
 }
 
diff --git a/services/tasks/service.go b/services/tasks/service.go
index 6db93b5f8..75904a98c 100644
--- a/services/tasks/service.go
+++ b/services/tasks/service.go
@@ -567,7 +567,10 @@ func (s *Service) writeContent(ctx context.Context, mediaType, ref string, r io.
 	if err != nil {
 		return nil, err
 	}
-	if err := writer.Commit(ctx, 0, ""); err != nil {
+	labels := map[string]string{
+		"containerd.io/gc.root": time.Now().UTC().Format(time.RFC3339),
+	}
+	if err := writer.Commit(ctx, 0, "", content.WithLabels(labels)); err != nil {
 		return nil, err
 	}
 	return &types.Descriptor{
diff --git a/spec_opts_unix.go b/spec_opts_unix.go
index 337095cfa..7009522d2 100644
--- a/spec_opts_unix.go
+++ b/spec_opts_unix.go
@@ -11,6 +11,7 @@ import (
 	"path/filepath"
 	"strconv"
 	"strings"
+	"time"
 
 	"golang.org/x/sys/unix"
 
@@ -20,6 +21,7 @@ import (
 	"github.com/containerd/containerd/images"
 	"github.com/containerd/containerd/namespaces"
 	"github.com/containerd/containerd/platforms"
+	"github.com/containerd/containerd/snapshot"
 	"github.com/opencontainers/image-spec/identity"
 	"github.com/opencontainers/image-spec/specs-go/v1"
 	"github.com/opencontainers/runc/libcontainer/user"
@@ -258,16 +260,19 @@ func withRemappedSnapshotBase(id string, i Image, uid, gid uint32, readonly bool
 			snapshotter = client.SnapshotService(c.Snapshotter)
 			parent      = identity.ChainID(diffIDs).String()
 			usernsID    = fmt.Sprintf("%s-%d-%d", parent, uid, gid)
+			opt         = snapshot.WithLabels(map[string]string{
+				"containerd.io/gc.root": time.Now().UTC().Format(time.RFC3339),
+			})
 		)
 		if _, err := snapshotter.Stat(ctx, usernsID); err == nil {
-			if _, err := snapshotter.Prepare(ctx, id, usernsID); err != nil {
+			if _, err := snapshotter.Prepare(ctx, id, usernsID, opt); err != nil {
 				return err
 			}
 			c.SnapshotKey = id
 			c.Image = i.Name()
 			return nil
 		}
-		mounts, err := snapshotter.Prepare(ctx, usernsID+"-remap", parent)
+		mounts, err := snapshotter.Prepare(ctx, usernsID+"-remap", parent, opt)
 		if err != nil {
 			return err
 		}
@@ -275,13 +280,13 @@ func withRemappedSnapshotBase(id string, i Image, uid, gid uint32, readonly bool
 			snapshotter.Remove(ctx, usernsID)
 			return err
 		}
-		if err := snapshotter.Commit(ctx, usernsID, usernsID+"-remap"); err != nil {
+		if err := snapshotter.Commit(ctx, usernsID, usernsID+"-remap", opt); err != nil {
 			return err
 		}
 		if readonly {
-			_, err = snapshotter.View(ctx, id, usernsID)
+			_, err = snapshotter.View(ctx, id, usernsID, opt)
 		} else {
-			_, err = snapshotter.Prepare(ctx, id, usernsID)
+			_, err = snapshotter.Prepare(ctx, id, usernsID, opt)
 		}
 		if err != nil {
 			return err
diff --git a/task.go b/task.go
index 0496b5953..bf830d2cf 100644
--- a/task.go
+++ b/task.go
@@ -17,6 +17,7 @@ import (
 	"github.com/containerd/containerd/content"
 	"github.com/containerd/containerd/diff"
 	"github.com/containerd/containerd/errdefs"
+	"github.com/containerd/containerd/log"
 	"github.com/containerd/containerd/mount"
 	"github.com/containerd/containerd/plugin"
 	"github.com/containerd/containerd/rootfs"
@@ -24,6 +25,7 @@ import (
 	google_protobuf "github.com/gogo/protobuf/types"
 	digest "github.com/opencontainers/go-digest"
 	"github.com/opencontainers/image-spec/specs-go/v1"
+	ocispec "github.com/opencontainers/image-spec/specs-go/v1"
 	specs "github.com/opencontainers/runtime-spec/specs-go"
 	"github.com/pkg/errors"
 )
@@ -486,7 +488,13 @@ func (t *task) checkpointTask(ctx context.Context, index *v1.Index, request *tas
 }
 
 func (t *task) checkpointRWSnapshot(ctx context.Context, index *v1.Index, snapshotterName string, id string) error {
-	rw, err := rootfs.Diff(ctx, id, t.client.SnapshotService(snapshotterName), t.client.DiffService(), diff.WithReference(fmt.Sprintf("checkpoint-rw-%s", id)))
+	opts := []diff.Opt{
+		diff.WithReference(fmt.Sprintf("checkpoint-rw-%s", id)),
+		diff.WithLabels(map[string]string{
+			"containerd.io/gc.root": time.Now().UTC().Format(time.RFC3339),
+		}),
+	}
+	rw, err := rootfs.Diff(ctx, id, t.client.SnapshotService(snapshotterName), t.client.DiffService(), opts...)
 	if err != nil {
 		return err
 	}
@@ -510,15 +518,32 @@ func (t *task) checkpointImage(ctx context.Context, index *v1.Index, image strin
 	return nil
 }
 
-func (t *task) writeIndex(ctx context.Context, index *v1.Index) (v1.Descriptor, error) {
+func (t *task) writeIndex(ctx context.Context, index *v1.Index) (d v1.Descriptor, err error) {
+	labels := map[string]string{
+		"containerd.io/gc.root": time.Now().UTC().Format(time.RFC3339),
+	}
+
+	for i, m := range index.Manifests {
+		labels[fmt.Sprintf("containerd.io/gc.ref.content.%d", i)] = m.Digest.String()
+		defer func(m ocispec.Descriptor) {
+			if err == nil {
+				info := content.Info{Digest: m.Digest}
+				if _, uerr := t.client.ContentStore().Update(ctx, info, "labels.containerd.io/gc.root"); uerr != nil {
+					log.G(ctx).WithError(uerr).WithField("dgst", m.Digest).Warnf("failed to remove root marker")
+				}
+			}
+		}(m)
+	}
+
 	buf := bytes.NewBuffer(nil)
 	if err := json.NewEncoder(buf).Encode(index); err != nil {
 		return v1.Descriptor{}, err
 	}
-	return writeContent(ctx, t.client.ContentStore(), v1.MediaTypeImageIndex, t.id, buf)
+
+	return writeContent(ctx, t.client.ContentStore(), v1.MediaTypeImageIndex, t.id, buf, content.WithLabels(labels))
 }
 
-func writeContent(ctx context.Context, store content.Store, mediaType, ref string, r io.Reader) (d v1.Descriptor, err error) {
+func writeContent(ctx context.Context, store content.Store, mediaType, ref string, r io.Reader, opts ...content.Opt) (d v1.Descriptor, err error) {
 	writer, err := store.Writer(ctx, ref, 0, "")
 	if err != nil {
 		return d, err
@@ -528,7 +553,7 @@ func writeContent(ctx context.Context, store content.Store, mediaType, ref strin
 	if err != nil {
 		return d, err
 	}
-	if err := writer.Commit(ctx, size, ""); err != nil {
+	if err := writer.Commit(ctx, size, "", opts...); err != nil {
 		return d, err
 	}
 	return v1.Descriptor{