If the smaller of your two files will fit into memory then load that into a hash with the id as the key. Then use a while loop to loop over the other file checking each id against the hash.

If neither will fit in memory then perhaps consider loading one of the files into a db. DBM::Deep, for example, is particularly suited to _big_ look ups. Then proceed as above.

Write some code, see how you get on and, if you get stuck show what you have and we'll help you with it. This way we'll have a better idea of the sort of help you need.

Good luck!