#!/usr/bin/perl
use strict;

my (%count, $occ);
my @files = ("file1", "file2", "file3");

# read all files sequentially
foreach my $file (@files) {
    open (IN, "<$file") || die "could not open $file\n";
    while (<IN>) {
        chomp;
        # if line contains specified string add it to 'file' and 'foun
+d string' specific array
        /(H\(\d+\))/ && do { push @{$count{$file}{$1}}, $_ }
    }
    close (IN);
}

# loop over files
foreach my $file (keys %count) {
    print "$file\n";
    # loop over found strings
    foreach my $found (keys %{$count{$file}}) {
        # count occurences
        $occ = scalar (@{$count{$file}{$found}});
        # print found lines if occured more than 1 time
        if ($occ > 1) {
            foreach (@{$count{$file}{$found}}) {
                print "$_\n";
            }
        }
    }
    print "\n";
}
[download]

file1:
N(8) -- H(15) .. O(9)
N(8) -- H(16) .. N(8)
N(8) -- H(16) .. O(9)

file2:
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
N(8) -- H(16) .. O(9)

file3:
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
N(8) -- H(16) .. O(9)
[download]

file1
N(8) -- H(16) .. N(8)
N(8) -- H(16) .. O(9)

file2
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)

file3
N(8) -- H(15) .. O(9)
N(8) -- H(15) .. N(8)
[download]

That is exactly what I'm trying to achieve. Although I already have all the lines of data stored in @contact_type.
All I need to do is iterate over @contact_type and check for the defind pattern and print if any are repeated.
Can the code you have provided be changed to do that ?
<br.cheers harry

Harry,
when you already have all the lines in @contact_type, you have no information ready about the source of your lines. (i.e. what file did it come from)
do you care about that?
If yes I'd suggest to change the reading through the files to a similar way I did it.
If no, tell me ...
Imre