Some of the deepest differences between Iran and Afghanistan are ideological and doctrinal. Iran's conservative religious leaders base their legitimacy on their Shiite strain of Islam, while the equally conservative Taliban leaders base theirs on the majority Sunni strain.

The two countries also have serious border disputes. Iran unwillingly plays host to about 1.4 million Afghan refugees, most congregated in camps near the frontier, and it is waging a violent campaign to seal its border to opium shipments from Afghanistan. Iran almost went to war with Afghanistan in 1998, when Taliban soldiers killed 10 Iranian diplomats and an Iranian journalist in the northern Afghanistan town of Mazar-e Sharif.

Some analysts have argued that the United States should try more forcefully to repair relations with Iran because it could play a role in containing hostile regimes in Afghanistan and Iraq, another of its neighbors.

The Islamic Republic of Iran is one of the few countries in the world that refuses to establish government-to-government ties with the United States, citing numerous historical grievances, particularly the CIA's role in a 1953 coup that overthrew an elected government and installed Shah Mohammad Reza Pahlavi as ruler. The shah was overthrown in the 1979 Islamic revolution, during which radical students seized the U.S. Embassy and held 52 U.S. Americans hostage for 444 days. Relations between the two countries have never recovered.