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--the good, the bad and the physi--
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mod_perl is a Perl interpreter embedded in an Apache server process, and requires the use of handlers and directives to control those handlers. mod_cgi is CGI: a language agnostic handler that forks a separate process to run a program, passing some information via environment variables and other information via standard input, expecting the response to come via standard output and an exit code.

Some CGI programs are written in Perl. But it's either mod_perl or mod_cgi handling it. Never both.

-- Randal L. Schwartz, Perl hacker
Be sure to read my standard disclaimer if this is a reply.

Just to make it a little more confusing the CGI module works with mod_perl as well as CGI.

However, unless you need your code to work in both CGI and mod_perl it's a better idea to use the various mod_perl packages directly (Apache::Request, etc.)