Why does The Doctor in Doctor Who have two hearts?

Answer 1

Well, The Doctor is from a race of aliens called Time Lords. A Time Lord possesses a binary vascular system, meaning that The Doctor's body is optimized to run on the extra strength and endurance that two hearts can give (hence the reason he can do things like run for a long time without getting tired).

Interestingly enough, in the episode 'The Shakespeare Code', the Doctor had one heart go out on him for a brief period of time. Instead of functioning at normal human capacities during that time, showed extreme weakness and pain. This suggests that the two different hearts, instead of supplying equal amounts of blood to the entire body, have different primary functions.

So, that's the long, sciencey, geeky answer. If you want the short answer-He's an alien. It's no wonder some of his internal workings are different than ours.