diff --git a/dvc/command/checkout.py b/dvc/command/checkout.py
index f163b934e..c251a04d5 100644
--- a/dvc/command/checkout.py
+++ b/dvc/command/checkout.py
@@ -1,6 +1,8 @@
 import os
 
 from dvc.command.common.base import CmdBase
+from dvc.command.common.cache_dir import CacheDir
+from dvc.config import ConfigI
 from dvc.logger import Logger
 from dvc.system import System
 
@@ -35,6 +37,23 @@ class CmdCheckout(CmdBase):
             Logger.info('Checkout \'{}\''.format(item.data.relative))
  
     def run(self):
+        self.remove_not_tracked_hardlinks()
         items = self.settings.path_factory.all_existing_data_items()
         self.checkout(items)
         return 0
+
+    def remove_not_tracked_hardlinks(self):
+        untracked_files = self.git.all_untracked_files()
+
+        cache_dir = os.path.join(self.git.git_dir_abs, ConfigI.CACHE_DIR)
+        cached_files = CacheDir(cache_dir).find_caches(untracked_files)
+
+        for file in cached_files:
+            Logger.info(u'Remove \'{}\''.format(file))
+            os.remove(file)
+
+            dir = os.path.dirname(file)
+            if not os.listdir(dir):
+                Logger.info(u'Remove empty directory \'{}\''.format(dir))
+                os.removedirs(dir)
+        pass
diff --git a/dvc/git_wrapper.py b/dvc/git_wrapper.py
index f9eb9d45c..1aee053c2 100644
--- a/dvc/git_wrapper.py
+++ b/dvc/git_wrapper.py
@@ -439,3 +439,11 @@ class GitWrapper(GitWrapperI):
     def get_file_content(fname, branch):
         cmd = 'git show {}:{}'.format(branch, fname)
         return Executor.exec_cmd_only_success(cmd.split())
+
+    @staticmethod
+    def all_untracked_files():
+        cmd = 'git ls-files --others --exclude-standard'
+        res = Executor.exec_cmd_only_success(cmd.split())
+        if not res.strip():
+            return []
+        return res.split('\n')