Ok, now try this with grep added

#!/usr/bin/perl
use strict;
my $t0 = time;

my $file1 = $ARGV[0] || 'ficc.txt';
my $file2 = $ARGV[1] || 'fic.txt';

my %uniq1=();
my $count1=0; my $words1=0;
open FICC,'<',$file1 or die "$file1 : $!";
while (<FICC>) {
  my @words = split /\s+/,lc $_;
  ++$uniq1{$_} for @words;
  $words1 += @words;
  ++$count1;
}
close FICC;
my $uniq1 = scalar keys %uniq1;

my %uniq2=();
my $count2=0; my $words2=0;
open FIC,'<',$file2 or die "$file2 : $!";
while (my $line = <FIC>) {
  my @words = split /\s+/,lc $line;
  ++$uniq2{$_} for @words;
  $words2 += @words;
  ++$count2;
  my @match = grep $uniq1{$_}, @words;
}
close FICC;
my $uniq2 = scalar keys %uniq2;

my $dur = int time-$t0;
print "
File1 : $count1 lines $words1 words $uniq1 unique in $file1
File2 : $count2 lines $words2 words $uniq2 unique in $file2
Time  : $dur seconds\n";
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These are the results for my i5-2500K

File1 : 4000000 lines 7998273 words 6379952 unique in ficc1.txt
File2 : 4000000 lines 11999843 words 9364684 unique in fic1.txt
Time  : 37 seconds

File1 : 3874004 lines 6050371 words 2413 unique in trans3 File2 : 4305242 lines 6457863 words 2313 unique in gh3-3.n Time : 96 seconds

i work with an old core2duo T7100, 1.8ghz

Add a print when at least 1 of the words match if that's the output you want

while (my $line = <FIC>) {
  my @words = split /\s+/,lc $line;
  ++$uniq2{$_} for @words;
  $words2 += @words;
  ++$count2;
  my @match = grep $uniq1{$_}, @words;
  print $line if @match >= 1; # <-- add here
}
[download]

poj