Given the choice, I usually opt for mod_perl. As mentioned above, CGI has a slower start-up time. If your application has high performance needs and you have full control of the server then I would suggest mod_perl. If it's a hosted server, or you don't measure your performance in milliseconds, then CGI will work just fine. The question you should be asking yourself is, what are the requirements of your application? That should dictate your decision.