diff --git a/gclient_scm.py b/gclient_scm.py
index 89647ac0e..b5a09a224 100644
--- a/gclient_scm.py
+++ b/gclient_scm.py
@@ -352,7 +352,8 @@ class GitWrapper(SCMWrapper):
         (os.path.isdir(self.checkout_path) and
          not os.path.exists(os.path.join(self.checkout_path, '.git')))):
       if (os.path.isdir(self.checkout_path) and
-          not os.path.exists(os.path.join(self.checkout_path, '.git'))):
+          not os.path.exists(os.path.join(self.checkout_path, '.git')) and
+          os.listdir(self.checkout_path)):
         # This is a little hack to work around checkouts which are created
         # using "gclient config --name ."
         if not self.relpath == '.':
diff --git a/tests/gclient_scm_test.py b/tests/gclient_scm_test.py
index c49b5247e..dbd94f0a7 100755
--- a/tests/gclient_scm_test.py
+++ b/tests/gclient_scm_test.py
@@ -1300,6 +1300,8 @@ class ManagedGitWrapperTestCaseMox(BaseTestCase):
     gclient_scm.os.path.isdir(self.base_path).AndReturn(True)
     gclient_scm.os.path.exists(os.path.join(self.base_path, '.git')
                                ).AndReturn(False)
+    self.mox.StubOutWithMock(gclient_scm.os, 'listdir', True)
+    gclient_scm.os.listdir(self.base_path).AndReturn([])
 
     self.mox.StubOutWithMock(gclient_scm.GitWrapper, '_Clone', True)
     # pylint: disable=E1120
@@ -1332,6 +1334,8 @@ class ManagedGitWrapperTestCaseMox(BaseTestCase):
     gclient_scm.os.path.isdir(self.base_path).AndReturn(True)
     gclient_scm.os.path.exists(os.path.join(self.base_path, '.git')
                                ).AndReturn(False)
+    self.mox.StubOutWithMock(gclient_scm.os, 'listdir', True)
+    gclient_scm.os.listdir(self.base_path).AndReturn([])
     self.mox.StubOutWithMock(gclient_scm.GitWrapper, '_Clone', True)
     # pylint: disable=E1120
     gclient_scm.GitWrapper._Clone('refs/remotes/origin/master', self.url,