When you say "works fine when I run it on the command line", does it output a proper header? Do you have print CGI::header(); or print "Content-type:text/html\n\n";, or some variant thereof in your script?

Other possibilities are that the webserver does not have both read and execute permissions on the file, or that your script depends crucially on some environment variable's being set a certain way in order to run.

Post your code, so we can get a better handle on your situation.

I mistrust all systematizers and avoid them. The will to a system shows a lack of integrity -- F. Nietzsche