The relationship between al-Qa`ida and Iran is shrouded in mystery. Before and after the September 11 attacks on the United States, al-Qa`ida operatives transited Iran, and some found sanctuary in the country after fleeing Afghanistan in late 2001. Yet the hints of occasional operational cooperation between al-Qa`ida and Iran are outweighed by the considerable and public evidence of the deep animosity between Sunni extremist al-Qa`ida and Shi`a extremist Iran. Antipathy for each other is at the root of their ideologies and narratives, and it has been most visible in their competition for influence in Iraq and Afghanistan.

This dynamic may change, however, if the United States and Iran move toward confrontation or even conflict over the Iranian government’s nuclear weapons ambitions. As tensions between Washington and Tehran increase, Shi`a antipathy for Sunni jihadists such as al-Qa`ida and its Taliban allies may be outweighed by a desire to find ways to spoil U.S. interests in the region. Similarly, as Washington ratchets up the pressure on al-Qa`ida in Pakistan, Usama bin Ladin and al-Qa`ida may find Iran a more attractive partner. Thus, what has been a hostile relationship could become a more collaborative one.

This article reviews the historical relationship between al-Qa`ida and Iran before examining the factors that could cause the two entities to work together against the United States and its allies.


The evidence for a secret relationship between al-Qa`ida and Iran is significant, but largely limited and the facts quite murky. The 9/11 Commission’s report concluded that there is evidence of contacts among al-Qa`ida, the Iranian government and Iran’s Lebanese Hizb Allah ally dating back to Usama bin Ladin’s years in Khartoum in the mid-1990s.[1] During this time, it is possible that Hizb Allah provided some training to future al-Qa`ida operatives, as Sudan was a watering hole for virtually every terrorist and extremist group in the Middle East. As a result, it would not be surprising for the nascent al-Qa`ida group to have encountered the Iranian Revolutionary Guard Corps (IRGC) and the Iranian Ministry of Intelligence (MOIS).

Some sources, including the 9/11 Commission, have suggested more than mere contact, alleging that the two may have collaborated in the attack on the U.S. Air Force barracks in Khobar, Saudi Arabia in 1996. In the CTC Sentinel, however, Thomas Hegghammer made clear that the evidence for such collaboration is unconvincing.[2] Moreover, evidence that emerged in the decade after the attack, reviewed by the author, also suggests that al-Qa`ida did not have involvement in the Khobar attacks.[3] Bin Ladin has said the same.[4]

The 9/11 Commission’s report also found that a senior Hizb Allah official visited Saudi Arabia in October 2000 to assist Saudis traveling to Afghanistan.[5] Three of the 9/11 hijackers reportedly traveled from Saudi Arabia to Beirut, then to Iran and into Afghanistan on a flight with an associate of a senior Hizb Allah official.[6] Khalid Shaykh Muhammad and Ramzi bin al-Shibh, two captured al-Qa`ida operatives, confirmed that 8-10 of the 9/11 hijackers at some point between October 2000 and February 2001 transited Iran on their way to or from Afghanistan “taking advantage of the Iranian practice of not stamping Saudi passports.”[7] What is not clear in the report is whether Iran gave these travelers any treatment different from that provided to other Saudis transiting Iran to Afghanistan in 2001.[8]

The bottom line of the 9/11 Commission’s report, however, is unequivocal. It states that both Khalid Shaykh Muhammad and Ramzi bin al-Shibh categorically denied any relationship between the hijackers and Hizb Allah. On Iran, the commission concluded, “we have found no evidence that Iran or Hizballah was aware of the planning for what later became the 9/11 attack.”[9]

After 9/11: Al-Qa`ida Operatives in Iran

After September 2001, several al-Qa`ida operatives, including one of Bin Ladin’s sons and other relatives, fled to Iran to escape the debacle of the collapse of the Islamic Emirate of Afghanistan. Some of these individuals have remained in Iran ever since. Their status has never been clear; some reports suggest they are under house arrest or even in prison. Other reports say they are free to operate. It has been reported that these Iran-based al-Qa`ida cells played a support role in the al-Qa`ida attacks on foreigners living in Riyadh on May 12, 2003 that killed 35 people, including eight Americans.[10] It has also been suggested that the Iranian government may be using its al-Qa`ida detainees as hostages to help dissuade the terrorist group from attacking Iranian interests. Tehran may also have hoped to trade them to the United States for Mujahidin-i-Khalq leaders captured in Iraq in 2003.[11] Their value to the Iranian government may change over time.

Bin Ladin’s son, Sa`ad, reportedly left Iran in 2008.[12] The circumstances are unclear about whether he was released by Iranian authorities or if he escaped. One of Bin Ladin’s daughters left Iran for Saudi Arabia this year via Syria.[13] After the U.S. invasion of Iraq in 2003, it is clear that al-Qa`ida messengers transited Iran to get from Pakistan to Iraq. The Iranian authorities apparently at least tolerated such transit if not facilitated it; they likely see such transfers as a relatively low risk method to keep the United States bogged down in two wars and therefore less likely to focus its attention on Iran.

Hostile Enemies?

On the other side of the ledger, the animosity between Iran and al-Qa`ida is public and abundantly clear. For al-Qa`ida and its allies such as the Taliban, Shi`a are not true Muslims and should be treated as outcasts at best, if not apostates. For Iran, the Taliban and al-Qa`ida are bigots who abuse Shi`a. The Taliban harshly repressed Afghan Hazara Shi`a in the 1990s, murdering thousands when it took over their towns and cities in 1998. The Taliban murdered several Iranian diplomats as well in 1998, and the two almost went to war over the incident.[14]

Al-Qa`ida was an enthusiastic and public supporter of the Taliban in its conflict with Tehran, a lonely voice of support at the time that probably helped cement Bin Ladin’s relationship with Taliban leader Mullah Omar. Al-Qa`ida provided troops and money for the fight against Iran’s Northern Alliance allies. The IRGC and MOIS were consistent supporters of al-Qa`ida’s Afghan enemy, the Northern Alliance, and had operatives in Afghanistan before and after 9/11. When the first Central Intelligence Agency team arrived in the Pansjhir Valley in late 2001 to overthrow the Taliban and al-Qa`ida, they found that the Iranians were already active in the area.[15]

Since 2003, al-Qa`ida’s franchise in Iraq has killed thousands of Iraqi Shi`a and scores of senior Shi`a leaders. Al-Qa`ida argues that the Shi`a are pawns of Iran seeking to restore “Safavid” control of the country, a reference to the first Shi`a Persian dynasty that fought the Ottoman Empire for control of Iraq in the 17th century. Al-Qa`ida’s first leader in Iraq,  Abu Mus`ab al-Zarqawi, was notoriously vicious in his hatred for the Shi`a, even earning a private reproach from Bin Ladin’s deputy, Ayman al-Zawahiri, for his indiscriminate attacks on Shi`a leaders, mosques and processions.

Al-Zarqawi wrote to al-Zawahiri to explain his view of the “heretic” Shi`a. It is worth looking at this letter, intercepted by U.S. intelligence, for an understanding of how al-Qa`ida views Iran and the Shi`a. Al-Zarqawi began by saying that the Shi`a are “an insurmountable obstacle, a lurking snake, a crafty and malicious scorpion, a spying enemy and a mortal venom.”[16] For al-Zarqawi, “Shiism is a looming danger and a true challenge that has nothing in common with Islam.”[17] Iran’s goal is to create a “heretical state from Iran through Iraq, Syria and Lebanon to the cardboard kingdom of the Gulf.”[18] He even quoted a European specialist as saying that if the “Safavids had not existed, we in Europe would be reading the Quran just as the Algerians do” because the Shi`a empire “stabbed the Muslims in the back” when the Ottomans were at the gates of Vienna in 1683.[19] Memories are long in al-Qa`ida.

During and since the 2006 war between Hizb Allah and Israel, al-Qa`ida leaders, including al-Zawahiri, have been critical of Hizb Allah for accepting a cease-fire with Israel and allowing United Nations peacekeepers to operate on Lebanese territory. Al-Qa`ida’s rebuke to Hizb Allah and Iran for being “soft” on Israel may strike many in the West as peculiar, but it is a visible manifestation of the depth of divide between the Sunni and Shi`a jihads. Since 2009, al-Qa`ida media outlets have reproached the Palestinian Sunni terrorist group Hamas for accepting aid from Iran in its fight with Israel.

On balance, the evidence of a hostile relationship is much more compelling than evidence for a collaborative one. Nevertheless, that does not preclude the possibility of occasional operational collusion; terrorists often seek help from criminals and drug dealers, and therefore from other terrorists as well. Yet it does not suggest a partnership or alliance.

Possible Change of Dynamics

This dynamic could change in the near future. The United States and Iran are on a collision course over Tehran’s determination to develop a nuclear weapons capability. As this confrontation worsens, Iran will be looking for ways to damage U.S. interests in the region, especially through means that bog the United States down further in Iraq and Afghanistan. Since the United States is withdrawing forces from Iraq, Afghanistan is probably the best venue to strike. Moreover, as the war in Afghanistan is now “Obama’s war”—where he has tripled U.S. troop numbers—the temptation to make the war harder may be impossible for Tehran to resist.

For several years, Iran has had a low-level relationship with its old nemesis, the Afghan Taliban. Since 2007, American and British commanders in Afghanistan have reported evidence of small quantities of Iranian arms provided to the Taliban and of the IRGC training Taliban operatives.[20] Iran has kept its options open in Afghanistan and has positioned itself to be more helpful to the Taliban should it decide to adopt this strategy. On the whole, Iran has been an ally of the Karzai government in Kabul since 2001 and has invested significantly in western Afghanistan to help stabilize the border region. For example, the largest Afghan city in the west, Herat, is linked to the Iranian electrical grid. Yet Iran could choose to “turn off the lights” if it wanted to make the already difficult Afghan mission even harder for the United States and NATO. The Italian military, which patrols Herat, is extremely conscious of its vulnerability to Iranian mischief.

Increasing aid to the Taliban while making life in western Afghanistan unpleasant for NATO would be a fairly simple and relatively low risk way of signaling to Washington that Iran can play hardball. Another path could be allowing al-Qa`ida greater use of Iranian territory for travel transit or safe haven. Indeed, to the extent that the United States puts pressure on al-Qa`ida’s safe haven in Pakistan, the terrorists will likely look for an alternative sanctuary. Iran is next door, and if allowed al-Qa`ida might find the change of venue attractive at least for parts of its infrastructure. While greater cooperation with the Taliban and al-Qa`ida could backfire and isolate Iran further, Tehran may consider the price worth paying in the face of Western aggression against its nuclear program.

Bruce Riedel is a Senior Fellow in the Saban Center for Middle East Policy at the Brookings Institution and a professor at Georgetown University. He has advised four U.S. presidents on Afghanistan and was asked by President Barack Obama in January 2009 to chair an interagency strategic review of American policy toward Afghanistan and Pakistan, which was completed in March 2009. He is the author of The Search for Al Qaeda: its Leadership, Ideology and Future.

[1]  The 9/11 Commission Report (New York: W.W. Norton & Co., 2004).

[2] Thomas Hegghammer, “Deconstructing the Myth about al-Qa`ida and Khobar,” CTC Sentinel 1:3 (2008).

[3]  The author was present at the Khobar Towers hours after the attack. During the next decade, the author reviewed all the available evidence on the attack and did not find an al-Qa`ida hand in the operation.

[4]  Bruce Lawrence ed., Messages to the World, The Statements of Osama Bin Laden (London: Verso, 2005), p. 52.

[5]  The 9/11 Commission Report.

[6]  Ibid.

[7]  Ibid.

[8]  Ibid.

[9]  Ibid.

[10]  Douglas Jehl and Eric Schmitt, “US Suggests a Qaeda Cell in Iran Directed Saudi Bombings,” New York Times, May 21, 2003.

[11]  The Mujahidin-i-Khalq is an organization that advocates the overthrow of the Islamic Republic of Iran.

[12]  “Bin Laden Son Saad Left Iran, Now in Pakistan-US,” Reuters, January 16, 2009.

[13]  “Bin Laden’s Daughter Set Free from Iran,” CBS/AP, March 23, 2010.

[14]  “Taliban Threatens Retaliation if Iran Strikes,” CNN, September 15, 1998.

[15]  Gary Schroen, First In: An Insider’s Account of How the CIA Spearheaded the War on Terror in Afghanistan (New York: Ballantine, 2006), p. 89.

[16]  “Text from Abu Mus’ab al-Zarqawi Letter,”, undated.

[17]  Ibid.

[18]  Ibid.

[19] “Letter to Bin Laden and Zawahiri,” in Gilles Kepel and Jean-Pierre Milelli eds., Al Qaeda in its Own Words (Cambridge, NJ: Harvard University Press, 2008), pp. 251-267.

[20]  Damien McElroy, “Iran Helping the Taliban, US Ambassador Claims,” Telegraph, December 17, 2009; Sajjan M. Gohel, “Iran’s Ambiguous Role in Afghanistan,” CTC Sentinel 3:3 (2010).

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