Only if you're using a broken/proprietary CGI parameter parsing routine that does something like this:

foreach my $pair (split /&/, $ENV{QUERY_STRING}) {
   my ($key, $value) = split(/=/, $pair);
   $parameters{$key} = $value;
}
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The correct solution is to defer processing like this to CGI.pm, which will correctly handle multiple checkboxes with the same name.