my @uniques = ();

my $md5;

while (my $string = <FILE>) {
  $md5 = md5hex $string;
  if (grep { $md5 eq $_ } @uniques) {
    warn "$string is not unique\n";
    # or push() into another list...
  }
  else {
    push @uniques, $md5;
  }
}

# Now @unique contains the list of unique strings