One way to achieve this is to use a Module for Apache, so each time Apache receives a request it will authenticate the user with the Domain and then make the user’s name available to your script in $ENV{REMOTE_USER} variable.
There are 2 modules that I know of. One is for Apache 1 (mod_ntlm) and the other is for Apache 2 (mod_sspi).
I have never used mod_ntlm, however use mod_sspi and Apache 2 in many cases with great success.
I believe that there are also some perl modules that you can use under mod_perl but I have never used any of them.
Hope this gives you some pointers.
Alistair
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