I'm using ActiveState Perl 5.6.1 with NT Server 4.0 and IIS. This article helped me configure my IIS/NT Server, but the REAL trick is to use .plx as the CGI script extension running out of your c:\Inetpub\wwwroot\cgi-bin directory. Give it a try; hope this works for you too!

Go see:  http://support.microsoft.com/support/kb/articles/Q150/6/29.asp

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