I was recently asked what the difference between CIL and MSIL is… the short answer is not much. They both describe the underlying CPU-independent instruction set the CLR executes after a high level language (C#, VB, C++, Python, Ruby, Pascal, etc) has compiled your source code. The difference between them is the exact version you are referring to.
CIL - Common Intermediate Language - is the term used in the International Standard.
MSIL - Microsoft Intermediate Language - is the product term for the Microsoft implementation of that standard.
Clear as mud?