diff --git a/dvc/cloud/base.py b/dvc/cloud/base.py
index 2bbb2beed4..7ea3400e53 100644
--- a/dvc/cloud/base.py
+++ b/dvc/cloud/base.py
@@ -125,8 +125,11 @@ def _push(self, path):
 
     def _makedirs(self, fname):
         dname = os.path.dirname(fname)
-        if not os.path.exists(dname):
+        try:
             os.makedirs(dname)
+        except OSError as e:
+            if e.errno != os.errno.EEXIST:
+                raise
 
     def _pull_key(self, key, path):
         """ Cloud-specific method of pulling keys """
diff --git a/dvc/project.py b/dvc/project.py
index 4674accdba..99363beeb4 100644
--- a/dvc/project.py
+++ b/dvc/project.py
@@ -159,14 +159,22 @@ def checkout(self):
         for stage in self.stages():
             stage.checkout()
 
-    def _used_cache(self):
+    def _used_cache(self, collect_dir=False):
         clist = []
         for stage in self.stages():
             for out in stage.outs:
                 if not out.use_cache:
                     continue
-                if out.cache not in clist:
+                if not os.path.isdir(out.cache) and \
+                   out.cache not in clist:
                     clist.append(out.cache)
+                if os.path.isdir(out.cache):
+                    dir_cache = out.dir_cache()
+                    clist.extend(dir_cache.values())
+                    if collect_dir:
+                        clist.extend([os.path.join(out.cache, f) for f in dir_cache.keys()])
+                    else:
+                        clist.append(out.cache)
         return clist
 
     def _remove_cache_file(self, cache):
@@ -188,7 +196,7 @@ def _remove_cache(self, cache):
         os.rmdir(cache)
 
     def gc(self):
-        clist = self._used_cache()
+        clist = self._used_cache(collect_dir=False)
         for cache in self.cache.all():
             if cache in clist:
                 continue
@@ -196,14 +204,14 @@ def gc(self):
             self.logger.info(u'\'{}\' was removed'.format(self.to_dvc_path(cache)))
 
     def push(self, jobs=1):
-        self.cloud.push(self._used_cache(), jobs)
+        self.cloud.push(self._used_cache(collect_dir=True), jobs)
 
     def pull(self, jobs=1):
-        self.cloud.pull(self._used_cache(), jobs)
+        self.cloud.pull(self._used_cache(collect_dir=False), jobs)
         self.checkout()
 
     def status(self, jobs=1):
-        return self.cloud.status(self._used_cache(), jobs)
+        return self.cloud.status(self._used_cache(collect_dir=True), jobs)
 
     def graph(self):
         G = nx.DiGraph()
diff --git a/tests/test_gc.py b/tests/test_gc.py
index 253d67c23a..82fdcdb32d 100644
--- a/tests/test_gc.py
+++ b/tests/test_gc.py
@@ -17,7 +17,8 @@ class TestGC(TestDvc):
     def setUp(self):
         super(TestGC, self).setUp()
 
-        stage = self.dvc.add(self.FOO)
+        self.dvc.add(self.FOO)
+        self.dvc.add(self.DATA_DIR)
         self.good_cache = self.dvc.cache.all()
 
         self.bad_cache = []
@@ -26,6 +27,11 @@ def setUp(self):
             self.create(path, i)
             self.bad_cache.append(path)
 
+        path = os.path.join(self.dvc.cache.cache_dir, '45', '6', 'data')
+        os.mkdir(os.path.dirname(path))
+        self.create(path, 'md5: "123"')
+        self.bad_cache.append(path)
+
     def test_api(self):
         self.dvc.gc()
         self._test_gc()
@@ -41,4 +47,3 @@ def _test_gc(self):
 
         for c in self.good_cache:
             self.assertTrue(os.path.exists(c))
-            self.assertTrue(os.path.isfile(c))