The common language runtime, also known as the CLR, is a virtual machine used as part of Microsoft's .NET framework. It takes CIL (common intermediate language) code — bytecode from compiled C#, VB.NET or other .NET source code — and converts it to machine native code.
The CLR uses just-in-time compilation to execute the compiled code of .NET applications regardless of what programming language was used. In doing so, it ensures proper memory management, type safety, exception handling, garbage collection, system security, and thread management.
Additional information on CLR is on the Common Language Runtime site from Microsoft.