Well then, since you didnt mention anything from $pid = $y->{'pubmed-id'}; print "$pid\n"; it must mean $pid = $pidArray->{'pubmed-id'}; is the hash. Try adding print pp($pid); after that and see what kind of clue it gives you

As choroba mentioned XML::Simple itself says "The use of this module in new code is discouraged. Other modules are available which provide more straightforward and consistent interfaces. In particular, XML::LibXML is highly recommended and XML::Twig is an excellent alternative."