Assuming you are running UNIX/sendmail, add an entry to the /etc/aliases file with a pipe to your Perl program, e.g.

autoresponder    "|/path/to/your/perlscript.pl"

Rebuild the aliases file (with the 'newalias' command), then any emails sent to autoresponder@your.domain will call your script. The email message can be read from standard input to get the From: header, then open a pipe back to sendmail to send a reply.

Hope this helps,

JJ