If you look closely at the papers that are published under an heading of Chemical Biology; more often than not, they involve small molecules that are incorporated into the biological systems by artificial means

Whereas Biological Chemistry could easily mean,' The Chemistry performed by the biological systems.'

Chemical Biology = The Biology of Chemicals?

Biological Chemistry = The Chemistry of Biology?

Interpreted as above supports Martins view. We also had this discussion at our Department and settled for Chemical Biology since we wished to have a chemistry emphasis.

I agree with Joseph Grim. Chemical biology is the same for me as medicinal chemistry. You do know your biological target and try to find /create drugs to treat them. Biological chemistry is biochemistry to me as well.

I also agree with Joseph Grim but have different opinion about Medicinal Chemistry. I think that Medicinal Chemistry can be a part of Chemical Biology. However, there are several other targets for solving biological puzzles with synthetic tools.

I refer to chemical biology as using chemical "tools" to study biological systems, eg chemical proteomics often involves compound-affinity based protein identification whereas chemical genetics often involves compound-sensitivity based gene identification. Often but not always.

Biological chemistry on the other hand I take as biochemistry on a systems level.

Medicinal chemistry is just synthetic chemistry with a therapeutic application in mind, it can be used to create the "tools".