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I have lot of asp.net 3.5 and IIS 7 applications hosted in my server. I am now trying to install .NET Framework 4.0 but I a need to know whether, it will effect my old applications or not?

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No it will not affect them. .net 4.0 and 2.0/3.5 run seamlessly side by side with each other.

In ASP.Net you will be able to set the runtime version on each APP Pool

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