The code you've showed appears to work fine for me - maybe $lines doesn't contain what you think it does? In this WebPerl live demo (requires a modern browser), I've shown how to use Data::Dumper to inspect data structures.

You should probably also heed the warning that Perl gives you: "Scalar value @val[2] better written as $val[2] "- the former is a "slice" and is not the best way to access a single array element.

Update: Code from WebPerl reproduced here:

use warnings;
use strict;
use Data::Dumper;
$Data::Dumper::Useqq=1;

my $lines = ["A,B,C","D,E,F","G,H,I"];
print Dumper($lines);
my @store;
foreach my $line (@$lines) {
    my @val = split(/\,/,$line);
    print Dumper(\@val);
    push (@store,@val[2]);
}
print Dumper(\@store);
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