diff --git a/core/commands/pin.go b/core/commands/pin.go
index 934c9a39dcb..0842b35cae1 100644
--- a/core/commands/pin.go
+++ b/core/commands/pin.go
@@ -330,7 +330,7 @@ func pinLsAll(typeStr string, ctx context.Context, n *core.IpfsNode) (map[string
 			if err != nil {
 				return nil, err
 			}
-			err = dag.EnumerateChildren(n.Context(), n.DAG, nd, ks)
+			err = dag.EnumerateChildren(n.Context(), n.DAG, nd, ks, false)
 			if err != nil {
 				return nil, err
 			}
diff --git a/core/corerepo/gc.go b/core/corerepo/gc.go
index 621b44d3936..9333bfa2638 100644
--- a/core/corerepo/gc.go
+++ b/core/corerepo/gc.go
@@ -6,6 +6,7 @@ import (
 
 	key "github.com/ipfs/go-ipfs/blocks/key"
 	"github.com/ipfs/go-ipfs/core"
+	mfs "github.com/ipfs/go-ipfs/mfs"
 	gc "github.com/ipfs/go-ipfs/pin/gc"
 	repo "github.com/ipfs/go-ipfs/repo"
 	humanize "gx/ipfs/QmPSBJL4momYnE7DcUyk2DVhD6rH488ZmHBGLbxNdhU44K/go-humanize"
@@ -71,10 +72,26 @@ func NewGC(n *core.IpfsNode) (*GC, error) {
 	}, nil
 }
 
+func BestEffortRoots(filesRoot *mfs.Root) ([]key.Key, error) {
+	rootDag, err := filesRoot.GetValue().GetNode()
+	if err != nil {
+		return nil, err
+	}
+	rootKey, err := rootDag.Key()
+	if err != nil {
+		return nil, err
+	}
+	return []key.Key{rootKey}, nil
+}
+
 func GarbageCollect(n *core.IpfsNode, ctx context.Context) error {
 	ctx, cancel := context.WithCancel(ctx)
 	defer cancel() // in case error occurs during operation
-	rmed, err := gc.GC(ctx, n.Blockstore, n.Pinning)
+	roots, err := BestEffortRoots(n.FilesRoot)
+	if err != nil {
+		return err
+	}
+	rmed, err := gc.GC(ctx, n.Blockstore, n.Pinning, roots)
 	if err != nil {
 		return err
 	}
@@ -93,7 +110,11 @@ func GarbageCollect(n *core.IpfsNode, ctx context.Context) error {
 }
 
 func GarbageCollectAsync(n *core.IpfsNode, ctx context.Context) (<-chan *KeyRemoved, error) {
-	rmed, err := gc.GC(ctx, n.Blockstore, n.Pinning)
+	roots, err := BestEffortRoots(n.FilesRoot)
+	if err != nil {
+		return nil, err
+	}
+	rmed, err := gc.GC(ctx, n.Blockstore, n.Pinning, roots)
 	if err != nil {
 		return nil, err
 	}
diff --git a/core/coreunix/add_test.go b/core/coreunix/add_test.go
index 1663e0388d5..7a43b634903 100644
--- a/core/coreunix/add_test.go
+++ b/core/coreunix/add_test.go
@@ -96,7 +96,7 @@ func TestAddGCLive(t *testing.T) {
 	gcstarted := make(chan struct{})
 	go func() {
 		defer close(gcstarted)
-		gcchan, err := gc.GC(context.Background(), node.Blockstore, node.Pinning)
+		gcchan, err := gc.GC(context.Background(), node.Blockstore, node.Pinning, nil)
 		if err != nil {
 			log.Error("GC ERROR:", err)
 			errs <- err
@@ -155,7 +155,7 @@ func TestAddGCLive(t *testing.T) {
 		t.Fatal(err)
 	}
 
-	err = dag.EnumerateChildren(ctx, node.DAG, root, key.NewKeySet())
+	err = dag.EnumerateChildren(ctx, node.DAG, root, key.NewKeySet(), false)
 	if err != nil {
 		t.Fatal(err)
 	}
diff --git a/merkledag/merkledag.go b/merkledag/merkledag.go
index 6792e3e51c5..4938e7bab11 100644
--- a/merkledag/merkledag.go
+++ b/merkledag/merkledag.go
@@ -357,16 +357,20 @@ func (t *Batch) Commit() error {
 // EnumerateChildren will walk the dag below the given root node and add all
 // unseen children to the passed in set.
 // TODO: parallelize to avoid disk latency perf hits?
-func EnumerateChildren(ctx context.Context, ds DAGService, root *Node, set key.KeySet) error {
+func EnumerateChildren(ctx context.Context, ds DAGService, root *Node, set key.KeySet, bestEffort bool) error {
 	for _, lnk := range root.Links {
 		k := key.Key(lnk.Hash)
 		if !set.Has(k) {
 			set.Add(k)
 			child, err := ds.Get(ctx, k)
 			if err != nil {
-				return err
+				if bestEffort && err == ErrNotFound {
+					continue
+				} else {
+					return err
+				}
 			}
-			err = EnumerateChildren(ctx, ds, child, set)
+			err = EnumerateChildren(ctx, ds, child, set, bestEffort)
 			if err != nil {
 				return err
 			}
diff --git a/merkledag/merkledag_test.go b/merkledag/merkledag_test.go
index 644d4e2d5ee..79b7399b57f 100644
--- a/merkledag/merkledag_test.go
+++ b/merkledag/merkledag_test.go
@@ -292,7 +292,7 @@ func TestFetchGraph(t *testing.T) {
 	offline_ds := NewDAGService(bs)
 	ks := key.NewKeySet()
 
-	err = EnumerateChildren(context.Background(), offline_ds, root, ks)
+	err = EnumerateChildren(context.Background(), offline_ds, root, ks, false)
 	if err != nil {
 		t.Fatal(err)
 	}
@@ -309,7 +309,7 @@ func TestEnumerateChildren(t *testing.T) {
 	}
 
 	ks := key.NewKeySet()
-	err = EnumerateChildren(context.Background(), ds, root, ks)
+	err = EnumerateChildren(context.Background(), ds, root, ks, false)
 	if err != nil {
 		t.Fatal(err)
 	}
diff --git a/pin/gc/gc.go b/pin/gc/gc.go
index 1a043c81778..34906fffb63 100644
--- a/pin/gc/gc.go
+++ b/pin/gc/gc.go
@@ -17,18 +17,19 @@ var log = logging.Logger("gc")
 // GC performs a mark and sweep garbage collection of the blocks in the blockstore
 // first, it creates a 'marked' set and adds to it the following:
 // - all recursively pinned blocks, plus all of their descendants (recursively)
+// - bestEffortRoots, plus all of its descendants (recursively)
 // - all directly pinned blocks
 // - all blocks utilized internally by the pinner
 //
 // The routine then iterates over every block in the blockstore and
 // deletes any block that is not found in the marked set.
-func GC(ctx context.Context, bs bstore.GCBlockstore, pn pin.Pinner) (<-chan key.Key, error) {
+func GC(ctx context.Context, bs bstore.GCBlockstore, pn pin.Pinner, bestEffortRoots []key.Key) (<-chan key.Key, error) {
 	unlocker := bs.GCLock()
 
 	bsrv := bserv.New(bs, offline.Exchange(bs))
 	ds := dag.NewDAGService(bsrv)
 
-	gcs, err := ColoredSet(ctx, pn, ds)
+	gcs, err := ColoredSet(ctx, pn, ds, bestEffortRoots)
 	if err != nil {
 		return nil, err
 	}
@@ -69,7 +70,7 @@ func GC(ctx context.Context, bs bstore.GCBlockstore, pn pin.Pinner) (<-chan key.
 	return output, nil
 }
 
-func Descendants(ctx context.Context, ds dag.DAGService, set key.KeySet, roots []key.Key) error {
+func Descendants(ctx context.Context, ds dag.DAGService, set key.KeySet, roots []key.Key, bestEffort bool) error {
 	for _, k := range roots {
 		set.Add(k)
 		nd, err := ds.Get(ctx, k)
@@ -78,7 +79,7 @@ func Descendants(ctx context.Context, ds dag.DAGService, set key.KeySet, roots [
 		}
 
 		// EnumerateChildren recursively walks the dag and adds the keys to the given set
-		err = dag.EnumerateChildren(ctx, ds, nd, set)
+		err = dag.EnumerateChildren(ctx, ds, nd, set, bestEffort)
 		if err != nil {
 			return err
 		}
@@ -87,11 +88,16 @@ func Descendants(ctx context.Context, ds dag.DAGService, set key.KeySet, roots [
 	return nil
 }
 
-func ColoredSet(ctx context.Context, pn pin.Pinner, ds dag.DAGService) (key.KeySet, error) {
+func ColoredSet(ctx context.Context, pn pin.Pinner, ds dag.DAGService, bestEffortRoots []key.Key) (key.KeySet, error) {
 	// KeySet currently implemented in memory, in the future, may be bloom filter or
 	// disk backed to conserve memory.
 	gcs := key.NewKeySet()
-	err := Descendants(ctx, ds, gcs, pn.RecursiveKeys())
+	err := Descendants(ctx, ds, gcs, pn.RecursiveKeys(), false)
+	if err != nil {
+		return nil, err
+	}
+
+	err = Descendants(ctx, ds, gcs, bestEffortRoots, true)
 	if err != nil {
 		return nil, err
 	}
@@ -100,7 +106,7 @@ func ColoredSet(ctx context.Context, pn pin.Pinner, ds dag.DAGService) (key.KeyS
 		gcs.Add(k)
 	}
 
-	err = Descendants(ctx, ds, gcs, pn.InternalPins())
+	err = Descendants(ctx, ds, gcs, pn.InternalPins(), false)
 	if err != nil {
 		return nil, err
 	}
diff --git a/test/sharness/t0252-files-gc.sh b/test/sharness/t0252-files-gc.sh
new file mode 100755
index 00000000000..416b020fddf
--- /dev/null
+++ b/test/sharness/t0252-files-gc.sh
@@ -0,0 +1,36 @@
+#!/bin/sh
+#
+# Copyright (c) 2016 Jeromy Johnson
+# MIT Licensed; see the LICENSE file in this repository.
+#
+
+test_description="test how the unix files api interacts with the gc"
+
+. lib/test-lib.sh
+
+test_init_ipfs
+
+test_expect_success "object not removed after gc" '
+  echo "hello world"  | ipfs files write --create /hello.txt &&
+  ipfs repo gc &&
+  ipfs cat QmVib14uvPnCP73XaCDpwugRuwfTsVbGyWbatHAmLSdZUS
+'
+
+test_expect_success "gc okay after adding incomplete node -- prep" '
+  ipfs files mkdir /adir &&
+  echo "file1" |  ipfs files write --create /adir/file1 &&
+  echo "file2" |  ipfs files write --create /adir/file2 &&
+  ipfs pin add --recursive=false QmbCgoMYVuZq8m1vK31JQx9DorwQdLMF1M3sJ7kygLLqnW &&
+  ipfs files rm -r /adir &&
+  ipfs repo gc && # will remove /adir/file1 and /adir/file2 but not /adir
+  ipfs files cp /ipfs/QmbCgoMYVuZq8m1vK31JQx9DorwQdLMF1M3sJ7kygLLqnW /adir &&
+  ipfs pin rm QmbCgoMYVuZq8m1vK31JQx9DorwQdLMF1M3sJ7kygLLqnW
+'
+
+test_expect_success "gc okay after adding incomplete node" '
+  ipfs refs QmbCgoMYVuZq8m1vK31JQx9DorwQdLMF1M3sJ7kygLLqnW &&
+  ipfs repo gc &&
+  ipfs refs QmbCgoMYVuZq8m1vK31JQx9DorwQdLMF1M3sJ7kygLLqnW
+'
+
+test_done