You see, is not that I'm not open to alternatives. Is just that I read a lot of foruns adressing this problem (of use variavles as variables name) and as much as I tried, I was unable to use hash of hashes to solve my needs.

So I wanted to use the dirt way because I needed to solve it fast. But YES, I would like to improve my code to not have to disable strict. And I am thankfull for your help.

So here is the code I'm using now. Any improvement is welcome.

#!/usr/bin/perl
#use strict;
use warnings;

my $input_data = << 'REPORT_OF_INPUT';
Bet01;;Bet05;;Bet06;;Bet12;;
230;238;101;103;138;146;112;116;;
230;238;101;103;146;146;108;112;;
224;238;0;0;146;146;110;118;;
238;238;0;0;146;146;112;114;;
REPORT_OF_INPUT

my @inputs = split "\n", $input_data;

my $line = shift @inputs;
$line =~ s/;;/;/g;
my @loci_codes = split ";", $line;

foreach $line ( @inputs )
{
  my @alelos = split ";", $line;
  foreach my $locus ( @loci_codes )
  {
    no strict 'refs';
    my $allele1 = shift @alelos;
    my $allele2 = shift @alelos;
    ${$locus}{$allele1} += 1;
    ${$locus}{$allele2} += 1;
  }
}

foreach $locus ( @loci_codes )
{
  foreach my $key ( keys ( %{$locus} ) )
  {
    print "$locus ", $key, " = ", $$locus{$key}, "\n";
  }
}
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I'm using the data inside the code here just to make it easier for decode. But in my real program the content of $input_data will come from an external file. So its content may vary.