my %count; while (my $line_1 = <$INFILE_1>){ $line_1 =~ s/\s+$//; $count{$line_1}++; } while (my $line_2 = <$INFILE_2>){ $line_2 =~ s/\s+$//; print $line_2, "\n" if $count{$line_2}; } # untested