When running on x64 hardware, you have two options. First, to run in native 64-bit mode. This means all the applications running need to be 64-bit. The second is to run worker processes in 32-bit mode, which means all applications need to be 32-bit. This gives you good compatibility and performance is really good too.
Here's how to install the 32-bit or 64-bit versions of ASP.NET, as well as the option you need to run for IIS to get them working. http://support.microsoft.com/kb/894435
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