last I checked (a few days ago) md5sum and Digest::MD5's md5_hex gave the same result on RHEL5/x86_64.

Checking right now md5sum and Digest::MD5's md5_hex give the same result on my debian linux / x86_32.

I can't compare the 64 bit result against the 32 bit one at the moment, though.

update: and yeah, some example data and code would probably help us help you. For all I know you're just passing Digest::MD5 the filename instead of the file's content.