From what I've gathered, disease was the primary cause of most native indian deaths, e.g. smallpox, chickenpox, typhus, etc. However I'm guessing the indigenous tribes weren't healthy all of the time; so what kind of diseases were indigenous to North America?
Not to discourage further answers, but I wrote an answer to a similar question on the disease load of the Americas before 1492 about a year ago. The only change I would make to that comment is the recent genetic evidence suggesting tuberculosis arriving in the New World via seals instead of the mycobacteria hitching a ride to the Americas with human hosts.
There's been theories that syphillis was brought to Europe as a result of Columbus's voyages and the sexual interactions between the crew and natives. There's been some back and forth over it, although I think the latest is that it's more likely that it actually was brought over from the new world.