diff -Naur a/src/md5sum.c b/src/md5sum.c
--- a/src/md5sum.c	2014-07-20 20:19:43.269800000 +0400
+++ b/src/md5sum.c	2014-07-20 20:19:48.714200000 +0400
@@ -392,6 +392,16 @@
      significant -- that includes leading and trailing white space.  */
   *file_name = &s[i];
 
+#if __CYGWIN__
+  /* But on cygwin, where \r is only permitted on managed mounts (and is
+     relatively rare anyways), strip it from the line end since older
+     cygwin releases (which includes practically all msys1 releases)
+     of coreutils mistakenly output md5sums in text mode.
+     \r is not a legal character for use in file names on W32 anyway. */
+  if (s[s_len - 1] == '\r')
+    s[--s_len] = '\0';
+#endif /* __CYGWIN__ */
+
   if (escaped_filename)
     return filename_unescape (&s[i], s_len - i) != NULL;