If you cannot rely on identical files having identical names, then you'll probably want to use some sort of digest function that gives identical file (contents) identical digest values. Then, at least you can compare only the files with the same digest, since those with differing digests cannot be identical. I haven't used the CPAN digest functions myself, but Gisle Aas is a reliable contributer (to say the least), so Digest::file is a good place to look for something that will do a fine job.