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We recently added a couple of wiki pages dealing with installing Mapserver under IIS: https://github.com/mapserver/mapserver/wiki/Installing-Mapserver-under-IIS-7.n-with-FastCGI https://github.com/mapserver/mapserver/wiki/Configuring-FastCGI-for-Mapserver-on-IIS-5.n-and-6.n-x86 These should get you started, unless you are using php-mapscript: in that case ...

This sounds like a common issue with ArcGIS Server 10 and IIS. Please follow the steps in the following whitepaper from Esri. These will configure the ArcGIS Web services and REST applications to run under a separate IIS application pool with the identity of the ArcGIS Web services user and disable per request impersonation. Configure ArcGIS Server REST ...