The history of comparing chimpanzee and human DNA similarities begins in 1975. King and Wilson estimate 99% similarity between chimpanzee and human DNA. PDF of Evolution at two levels in humans and chimpanzees by King and Wilson.
On the same note, The fickle Y chromosome compares the Y chromosome in chimps to the Y chromosome in humans.
In summary: The Y chromosome in the Chimp is very, very different to the Y chromosome of Humans. This is interesting because the rest of the genome is very, very similar. There are probably two reasons for this:
Reason The First: The Y chromosome doesn’t have a partner during cell devision, so over time the DNA can be subjected to large change.
Reason The Second: The Y chromosome is in charge of sperm production, and because of the mating habits of chimps (where they have many, many partners, and lots and lots of sex) means that it’s a hotspot (so to speak) of selective pressure. Basically: the better your sperm, the more likely it’s going to reach the egg before someone elses.