IL, or Intermediate Language, is a CPU independent partially compiled code. IL code will be compiled to native machine code using current environmental properties by Just-In-Time compiler (JIT). JIT compiler translates the IL code to an assembly code and uses the CPU architecture of the target machine to execute a .NET application. In .NET, IL is called Common Intermediate Language (CIL), and in the early .NET days it was called Microsoft Intermediate Language (MSIL).

CLI, or Common Language Infrastructure, is an open specification developed by Microsoft. It is a compiled code library used for deployment, versioning, and security. In .NET there are two CLI types: process assemblies (EXE) and library assemblies (DLL). CLI assemblies contain code in CIL, and as mentioned, during compilation of CLI programming languages, the source code is translated into CIL code rather than into platform or processor specific object code.

To summarize:

When compiled, source code is first translated to IL (in .NET, that is CIL, and previously called MSIL).
CIL is then assembled into a bytecode and a CLI assembly is created.
Before code execution, CLI code is passed through the runtime’s JIT compiler to generate native machine code.
The computer’s processor executes the native machine code.