diff --git a/Lib/distutils/filelist.py b/Lib/distutils/filelist.py
--- a/Lib/distutils/filelist.py
+++ b/Lib/distutils/filelist.py
@@ -328,8 +328,9 @@ def translate_pattern(pattern, anchor=1,
         # ditch end of pattern character
         empty_pattern = glob_to_re('')
         prefix_re = glob_to_re(prefix)[:-len(empty_pattern)]
-        # paths should always use / in manifest templates
-        pattern_re = "^%s/.*%s" % (prefix_re, pattern_re)
+        pattern_re = ".*" + pattern_re
+        # need to escape os.sep for Windows
+        pattern_re = "^" + re.escape(os.sep).join((prefix_re, pattern_re))
     else:                               # no prefix -- respect anchor flag
         if anchor:
             pattern_re = "^" + pattern_re
diff --git a/Lib/distutils/tests/test_filelist.py b/Lib/distutils/tests/test_filelist.py
--- a/Lib/distutils/tests/test_filelist.py
+++ b/Lib/distutils/tests/test_filelist.py
@@ -1,6 +1,7 @@
 """Tests for distutils.filelist."""
 import re
 import unittest
+from os.path import join
 from distutils import debug
 from distutils.log import WARN
 from distutils.errors import DistutilsTemplateError
@@ -14,6 +15,7 @@ include ok
 include xo
 exclude xo
 include foo.tmp
+include buildout.cfg
 global-include *.x
 global-include *.txt
 global-exclude *.tmp
@@ -53,15 +55,19 @@ class FileListTestCase(support.LoggingSi
 
         # simulated file list
         file_list.allfiles = ['foo.tmp', 'ok', 'xo', 'four.txt',
-                              'global/one.txt',
-                              'global/two.txt',
-                              'global/files.x',
-                              'global/here.tmp',
-                              'f/o/f.oo',
-                              'dir/graft-one',
-                              'dir/dir2/graft2',
-                              'dir3/ok',
-                              'dir3/sub/ok.txt',
+                              'buildout.cfg',
+                              # filelist does not filter out VCS directories,
+                              # it's sdist that does
+                              join('.hg', 'last-message.txt'),
+                              join('global', 'one.txt'),
+                              join('global', 'two.txt'),
+                              join('global', 'files.x'),
+                              join('global', 'here.tmp'),
+                              join('f', 'o', 'f.oo'),
+                              join('dir', 'graft-one'),
+                              join('dir', 'dir2', 'graft2'),
+                              join('dir3', 'ok'),
+                              join('dir3', 'sub', 'ok.txt'),
                               ]
 
         for line in MANIFEST_IN.split('\n'):
@@ -69,8 +75,10 @@ class FileListTestCase(support.LoggingSi
                 continue
             file_list.process_template_line(line)
 
-        wanted = ['ok', 'four.txt', 'global/one.txt', 'global/two.txt',
-                  'f/o/f.oo', 'dir/graft-one', 'dir/dir2/graft2']
+        wanted = ['ok', 'buildout.cfg', 'four.txt',
+                  join('.hg', 'last-message.txt'), join('global', 'one.txt'),
+                  join('global', 'two.txt'), join('f', 'o', 'f.oo'),
+                  join('dir', 'graft-one'), join('dir', 'dir2', 'graft2')]
 
         self.assertEqual(file_list.files, wanted)
 
diff --git a/Lib/distutils/tests/test_sdist.py b/Lib/distutils/tests/test_sdist.py
--- a/Lib/distutils/tests/test_sdist.py
+++ b/Lib/distutils/tests/test_sdist.py
@@ -42,6 +42,7 @@ setup(name='fake')
 MANIFEST = """\
 # file GENERATED by distutils, do NOT edit
 README
+buildout.cfg
 inroot.txt
 setup.py
 data%(sep)sdata.dt
@@ -209,11 +210,18 @@ class SDistTestCase(PyPIRCCommandTestCas
         self.write_file((data_dir, 'data.dt'), '#')
         some_dir = join(self.tmp_dir, 'some')
         os.mkdir(some_dir)
+        # make sure VCS directories are pruned (#14004)
+        hg_dir = join(self.tmp_dir, '.hg')
+        os.mkdir(hg_dir)
+        self.write_file((hg_dir, 'last-message.txt'), '#')
+        # a buggy regex used to prevent this from working on windows (#6884)
+        self.write_file((self.tmp_dir, 'buildout.cfg'), '#')
         self.write_file((self.tmp_dir, 'inroot.txt'), '#')
         self.write_file((some_dir, 'file.txt'), '#')
         self.write_file((some_dir, 'other_file.txt'), '#')
 
         dist.data_files = [('data', ['data/data.dt',
+                                     'buildout.cfg',
                                      'inroot.txt',
                                      'notexisting']),
                            'some/file.txt',
@@ -243,15 +251,15 @@ class SDistTestCase(PyPIRCCommandTestCas
             zip_file.close()
 
         # making sure everything was added
-        self.assertEqual(len(content), 11)
+        self.assertEqual(len(content), 12)
 
         # checking the MANIFEST
         f = open(join(self.tmp_dir, 'MANIFEST'))
         try:
             manifest = f.read()
-            self.assertEqual(manifest, MANIFEST % {'sep': os.sep})
         finally:
             f.close()
+        self.assertEqual(manifest, MANIFEST % {'sep': os.sep})
 
     @unittest.skipUnless(zlib, "requires zlib")
     def test_metadata_check_option(self):