I am currently doing this in win... i know... i have no choice though.

Ok. You can install any of the following:

• Cygwin at http://www.cygwin.com
• a bunch of natively ported utilies from http://unxutils.sourceforge.net/
• Microsoft's own Services for Unix at http://www.microsoft.com/windows/sfu/default.asp

All three have comm and sort and work just fine.

Yes that is about exactly how i was doing it, i am testing borisz way now and that looks really fast!

There are two problems with the algorithm I outlined. The second problem is bigger than the first

1. You are doing N iterations over the second array
2. You are reading the second file N times

The reason problem #2 is bigger is because I/O is extremely expensive. The following is an intermediate solution between borisz's excellent answer and your first algorithm. Even though I'm still iterating over the inner loop N times, I'm doing it in memory, which is much faster.

open my $fh1, 'first.csv';
my @first = <$fh1>;
close $fh1;

open my $fh2, 'second.csv';
my @second = <$fh1>;
close $fh2;

FIRST:
foreach my $line (@first) {
    foreach my $otherline (@second) {
        if ( $line eq $otherline ) {
            print "Found a duplicate!\n";
            next FIRST;
        }
    }
}
[download]

Note that I've also added short-circuiting to stop comparing the inner-loop when I've found a dupe. This will reduce the runtime quite a bit. The hash solution is still faster, and will take less memory.