In the .NET world IL, MSIL, and CIL all refer to the compiled output of .NET languages.

• IL - Intermediate Language
• MSIL - Microsoft Intermediate Language
• CIL - Common Intermediate Language

In most cases CIL is the best nomenclature to use of the three. This is because IL can have other meanings in other contexts 1, and MSIL isn't mentioned in the standards 2.

As a side note CIL isn't able to be executed directly. Instead it relies on a second compiler to turn it into proper assembly code for the machine it is running on. There are currently three main CIL to Assembly compilers: Microsoft's CLR (aka JIT), Microsoft's NGEN pre-compiler and Xamarin's Mono project (also a JIT).