You should also be using a hash, since this drastically decreases the number of comparisons required. The following works (tested it using sample data):
use strict;
use warnings;
my (%h, $handle);
open($handle, 'file1.txt');
while (<$handle>) {
# Creates hash using first field of each line as keys
$h{(split /,/)[0]} = ();
}
close($handle);
open($handle, 'file2.txt');
while (<$handle>) {
# Prints second field of each line if it exists in the hash
chomp; print "$_\n" if exists $h{$_ = (split /,/)[1]};
}
close($handle);
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