diff --git a/pre_commit/main.py b/pre_commit/main.py
index ce16acde..7092a5a8 100644
--- a/pre_commit/main.py
+++ b/pre_commit/main.py
@@ -8,6 +8,7 @@ import pkg_resources
 
 from pre_commit import color
 from pre_commit import five
+from pre_commit import git
 from pre_commit.commands.autoupdate import autoupdate
 from pre_commit.commands.clean import clean
 from pre_commit.commands.install_uninstall import install
@@ -110,7 +111,8 @@ def main(argv=None):
         help='Run on all the files in the repo.  Implies --no-stash.',
     )
     run_mutex_group.add_argument(
-        '--files', nargs='*', help='Specific filenames to run hooks on.',
+        '--files', nargs='*', default=[],
+        help='Specific filenames to run hooks on.',
     )
 
     help = subparsers.add_parser(
@@ -122,6 +124,11 @@ def main(argv=None):
     if len(argv) == 0:
         argv = ['run']
     args = parser.parse_args(argv)
+    if args.command == 'run':
+        args.files = [
+            os.path.relpath(os.path.abspath(filename), git.get_root())
+            for filename in args.files
+        ]
 
     if args.command == 'help':
         if args.help_cmd:
diff --git a/pre_commit/runner.py b/pre_commit/runner.py
index 88028939..35ab3427 100644
--- a/pre_commit/runner.py
+++ b/pre_commit/runner.py
@@ -24,7 +24,7 @@ class Runner(object):
     def create(cls):
         """Creates a PreCommitRunner by doing the following:
             - Finds the root of the current git repository
-            - chdirs to that directory
+            - chdir to that directory
         """
         root = git.get_root()
         os.chdir(root)
diff --git a/tests/commands/run_test.py b/tests/commands/run_test.py
index 363743fb..d4e37f20 100644
--- a/tests/commands/run_test.py
+++ b/tests/commands/run_test.py
@@ -83,7 +83,8 @@ def _do_run(repo, args, environ={}):
     runner = Runner(repo)
     write_mock = mock.Mock()
     write_fn = functools.partial(sys_stdout_write_wrapper, stream=write_mock)
-    ret = run(runner, args, write=write_fn, environ=environ)
+    with cwd(runner.git_root):  # replicates Runner.create behaviour
+        ret = run(runner, args, write=write_fn, environ=environ)
     printed = get_write_mock_output(write_mock)
     return ret, printed
 
@@ -595,3 +596,26 @@ def test_unstaged_message_suppressed(
     args = _get_opts(**opts)
     ret, printed = _do_run(modified_config_repo, args)
     assert b'Your .pre-commit-config.yaml is unstaged.' not in printed
+
+
+def test_files_running_subdir(
+        repo_with_passing_hook, mock_out_store_directory, tempdir_factory,
+):
+    with cwd(repo_with_passing_hook):
+        install(Runner(repo_with_passing_hook))
+
+        os.mkdir('subdir')
+        open('subdir/foo.py', 'w').close()
+        cmd_output('git', 'add', 'subdir/foo.py')
+
+        with cwd('subdir'):
+            # Don't want to write to home directory
+            env = dict(os.environ, PRE_COMMIT_HOME=tempdir_factory.get())
+            # Use subprocess to demonstrate behaviour in main
+            _, stdout, _ = cmd_output(
+                sys.executable, '-m', 'pre_commit.main', 'run', '-v',
+                # Files relative to where we are (#339)
+                '--files', 'foo.py',
+                env=env,
+            )
+        assert 'subdir/foo.py' in stdout