diff --git a/registry/storage/garbagecollect.go b/registry/storage/garbagecollect.go
index 317c792da..887f35238 100644
--- a/registry/storage/garbagecollect.go
+++ b/registry/storage/garbagecollect.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 
 	"github.com/docker/distribution"
+	"github.com/docker/distribution/manifest/schema2"
 	"github.com/docker/distribution/reference"
 	"github.com/docker/distribution/registry/storage/driver"
 	"github.com/opencontainers/go-digest"
@@ -25,6 +26,7 @@ type ManifestDel struct {
 	Name   string
 	Digest digest.Digest
 	Tags   []string
+	Layers []digest.Digest
 }
 
 // MarkAndSweep performs a mark and sweep of registry data
@@ -61,6 +63,11 @@ func MarkAndSweep(ctx context.Context, storageDriver driver.StorageDriver, regis
 		}
 
 		err = manifestEnumerator.Enumerate(ctx, func(dgst digest.Digest) error {
+			manifest, err := manifestService.Get(ctx, dgst)
+			if err != nil {
+				return fmt.Errorf("failed to retrieve manifest for digest %v: %v", dgst, err)
+			}
+
 			if opts.RemoveUntagged {
 				// fetch all tags where this manifest is the latest one
 				tags, err := repository.Tags(ctx).Lookup(ctx, distribution.Descriptor{Digest: dgst})
@@ -76,7 +83,23 @@ func MarkAndSweep(ctx context.Context, storageDriver driver.StorageDriver, regis
 					if err != nil {
 						return fmt.Errorf("failed to retrieve tags %v", err)
 					}
-					manifestArr = append(manifestArr, ManifestDel{Name: repoName, Digest: dgst, Tags: allTags})
+
+					manifestDel := ManifestDel{
+						Name:   repoName,
+						Digest: dgst,
+						Tags:   allTags,
+						Layers: []digest.Digest{},
+					}
+
+					for _, ref := range manifest.References() {
+						if ref.MediaType == schema2.MediaTypeLayer ||
+							ref.MediaType == schema2.MediaTypeImageConfig {
+							manifestDel.Layers = append(manifestDel.Layers, ref.Digest)
+						}
+					}
+
+					manifestArr = append(manifestArr, manifestDel)
+
 					return nil
 				}
 			}
@@ -84,11 +107,6 @@ func MarkAndSweep(ctx context.Context, storageDriver driver.StorageDriver, regis
 			emit("%s: marking manifest %s ", repoName, dgst)
 			markSet[dgst] = struct{}{}
 
-			manifest, err := manifestService.Get(ctx, dgst)
-			if err != nil {
-				return fmt.Errorf("failed to retrieve manifest for digest %v: %v", dgst, err)
-			}
-
 			descriptors := manifest.References()
 			for _, descriptor := range descriptors {
 				markSet[descriptor.Digest] = struct{}{}
@@ -122,6 +140,14 @@ func MarkAndSweep(ctx context.Context, storageDriver driver.StorageDriver, regis
 			if err != nil {
 				return fmt.Errorf("failed to delete manifest %s: %v", obj.Digest, err)
 			}
+			for _, layerDgst := range obj.Layers {
+				if _, ok := markSet[layerDgst]; !ok {
+					err := vacuum.RemoveLayerLink(obj.Name, layerDgst)
+					if err != nil {
+						return fmt.Errorf("failed to delete layer link %s for manifest %s: %v", layerDgst, obj.Name, err)
+					}
+				}
+			}
 		}
 	}
 	blobService := registry.Blobs()
diff --git a/registry/storage/vacuum.go b/registry/storage/vacuum.go
index a43db17a4..74e581a2d 100644
--- a/registry/storage/vacuum.go
+++ b/registry/storage/vacuum.go
@@ -84,6 +84,28 @@ func (v Vacuum) RemoveManifest(name string, dgst digest.Digest, tags []string) e
 	return v.driver.Delete(v.ctx, manifestPath)
 }
 
+// RemoveLayerLink removes a layer link from the filesystem
+func (v Vacuum) RemoveLayerLink(manifestName string, dgst digest.Digest) error {
+	layerLinkPath, err := pathFor(layerLinkPathSpec{name: manifestName, digest: dgst})
+	if err != nil {
+		return err
+	}
+
+	dcontext.GetLogger(v.ctx).Infof("Deleting layer link path : %s", layerLinkPath)
+
+	_, err = v.driver.Stat(v.ctx, layerLinkPath)
+	if err != nil {
+		switch err := err.(type) {
+		case driver.PathNotFoundError:
+			return nil
+		default:
+			return err
+		}
+	}
+
+	return v.driver.Delete(v.ctx, layerLinkPath)
+}
+
 // RemoveRepository removes a repository directory from the
 // filesystem
 func (v Vacuum) RemoveRepository(repoName string) error {