My wife and I took the "Scavi Tour" under the Vatican. To make a long story short, the bones of St Peter are down there. The dirt samples, the dating, the age of the skeleton, the location, and the evidence of purple fibers suggests that this is the Apostle.
One interesting thing about the bones is that the feet are missing! However, when we consider that sacred tradition teaches that St Peter was crucified head down. It is likely that the Romans merely hacked off the feet in order to remove the upside down body. And thus the feet never made it to the burial site.
Also, a piece of plaster from the repository in which the bones were found reads in Greek: PETROS ENI or "Peter in here." If you go to Rome, be sure to get the Scavi Tour. It is the worth the cost of the airfare.