Five times. In 17 episodes.
- Killed by an Eknodyne in Amy's Choice (Dream)
- Killed when the Doctor exploded the TARDIS in Amy's Choice (Dream)
- Shot by Restac, erased from time in "Cold Blood"
- Auton Rory was killed following Big Bang 2 in "The Big Bang"
- Drowned in "The Curse of the Black Spot"
- Waited 2000 years for Amy in the TARDIS and died in the Doctor's Wife (However, this was an illusion created by House to mess with Amy's mind)
He was also nearly killed by the Silents in The Wedding of River Song.