I'm 99.2718% sure the only package name munging done is on the ones automagically created by Apache::Registry around the programs it handles. Any modules you require from your code (e.g. CGI or Your::OtherPackage) aren't munged in any way and are shared between everything (that's kinda the whole point of mod_perl keeping the interpreter persistent). If your modules need to keep some server specific state you'll need to do something like passing them $r and keying off that.