[Solved] What is the best practice in checking the MD5 hashes of the .NET framework assemblies to avoid rootkit?

And check the file integrity?

Are you downloading it from places other that Microsoft?

From Microsoft. Use SSL to download. There is no way to tell that Microsoft has introduced a rootkit as hashes only spot changes, not malicious changes. Plus you would be getting the hash from Microsoft.

Any hashing tool will work https://support.microsoft.com/en-us/kb/889768

But you should avoid MD5 and go for SHA1 or above.

Thanks Nathan