From the New York Times why Sunnis and Shiites have been at war since the 7th century.

"The Sunni and Shiite branches of Islam split in the late seventh century in a dispute over whether the Prophet Mohammed's son-in-law, Ali, should carry on as the fourth caliph, or successor. The Shiites - meaning partisans or supporters of Ali - lost, and since then have been a kind of underclass in the Islamic world, nurturing an emotional faith with an emphasis on martyrdom."

http://www.nytimes.com/1987/08/02/world/400-die-iranian-marchers-battle-saudi-police-mecca-embassies-smashed-teheran.html?pagewanted=2