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As the U.S. and the West continue negotiations with Iran over its controversial nuclear program, the specter of Iran’s ties to terrorism - and specifically al-Qaida - lingers in the background, analysts and U.S. officials say.

“This is something that has gone back several decades now, but continues to get short shrift from the U.S. government,” said Jonathan Schanzer at the Foundation for Defense of Democracies.

“Iran’s playing three dimensional chess,” he said. “We see al-Qaida becomes useful to Iran in terms of attacking the United States, attacking the West, vilifying and targeting Israel. All these things very much work in Iran’s favor.”

For the past several years, the only U.S. government agency to consistently make the case linking Iran to al-Qaida has been the Treasury Department, which in February designated an Iran-based terrorist, Jafar al-Uzbeki, as a key al-Qaida facilitator. The designation accused him of funneling a “significant amount” of money from Iran into Afghanistan and Pakistan to help fund al-Qaida activities.

The designation also linked al-Uzbeki to Yasin al-Suri, previously identified as the head of al-Qaida’s Iran network and one of a handful of operatives identified since 2011 for getting al-Qaida fighters into Syria. And according to a senior Treasury official, al-Uzbeki has been “operating with the knowledge of the Iranian authorities.”

“This really deserves attention,” said U.S. Representative Adam Schiff, a member of the House Intelligence Committee. “We see a relationship between Iran and al-Qaida that at times is difficult to figure out, because on the one hand they would be natural adversaries, but in that part of the world, terrorism makes strange bedfellows.”

Still, the apparent union is between two opposing branches of Islam -- Shi’ite Iran and Sunni al-Qaida. It runs contrary to conventional wisdom, analysts say, as Shi’ites and Sunnis have targeted each other through violence across the Middle East.

Al-Qaida-linked groups targeted Iran late last year, killing 23 people, including a cultural attaché, in an attack on Tehran’s embassy in Lebanon.

“Ultimately the enmity between Iran and al-Qaida is almost deeper than the enmity between the United States and al-Qaida,” said Trita Parsi, founder and president of the National Iranian American Council. “But Iran is stuck in the region, and as a result sometimes it does strike small deals in order to actually protect itself or to advance its interests in other ways.”

Parsi said that in 2003, Iran was willing to trade al-Qaida operatives it caught fleeing from U.S. forces in Afghanistan to the United States in exchange for several concessions, a deal Washington rejected.

Yet not everyone is convinced the relationship between Iran and al-Qaida is one of forced convenience.

Investigators looking at the September 11, 2001 terrorist attacks on the U.S. raised concerns in their final report, pointing to “discussions in Sudan between al-Qaida and Iranian operatives” in the early 1990s.

“We thought it was an important question but you could not investigate every important question that arose from 9/11 fully,” said 9/11 commission co-chair and former congressman Lee Hamilton. “We had recommended in our report that the United States government further investigate the links between Iran and al-Qaida, including any collaboration prior to 9/11. To my knowledge the United States government has not done so.”

The 9/11 commission’s report cited possible collaboration between Iran and al-Qaida in the June 1996 attack on Khobar Towers, a residential complex housing American Air Force personnel in Dhahran, Saudi Arabia. Nineteen Americans were killed and 372 wounded.

The commission also turned up evidence suggesting Iran gave passage to the 9/11 hijackers, although commission member and former CIA operative Mike Hurley said there never was anything to suggest a larger role for Tehran in the attacks on the World Trade Center and the Pentagon.

“We could never establish that there was Iranian participation, Iranian government participation in the 9/11 plots,” Hurley said. But he added “there was a pattern of being open and welcoming to al-Qaida members, and sometimes even some senior figures of the al-Qaida shura [council] in Afghanistan.”

Hurley, who now serves as an advisor to the Bipartisan Policy Center in Washington, is among those who hoped the U.S. government would have done more to clarify the nature of the Iran-al-Qaida relationship.

“I don’t have a good sense and I don’t know that there’s been kind of deep active pursuit and investigation of that. I think it may be an area where the government has fallen down to some extent,” he said.

More recently, Canadian investigators alleged that two men arrested in connection with a 2013 plot to derail a train, Raed Jaser and Chiheb Esseghaier, received "directions and guidance" from members of al-Qaida in Iran. Iran denied any involvement.

U.S. officials also have said former al-Qaida spokesman Suleiman Abu Ghaith, now being tried on terror charges in the U.S., spent time in Iran along with one of former al-Qaida leader Osama bin Laden’s sons, Saad. The Iranian government claimed the two were “in custody,” but U.S. officials say Abu Ghaith was arrested last year in Jordan.

Still, despite the numerous concerns and the terrorist designations from the Treasury Department, officials at the State Department remain focused on the nuclear negotiations with Tehran, mentioning only their broad concerns about Iran’s ties to terror.

“While we are continuing engagement on the nuclear program and our concerns about that in a comprehensive deal, we have remaining concerns about human rights violations, about terrorist activities that they are up to,” State Department spokeswoman Jen Psaki said last week. “Certainly, I don’t think there’s a secret about our concerns, given we expressed them very publicly, about Iran’s engagement and efforts to assist Hezbollah and others who are encroaching into Syria.”

That approach concerns the Foundation for Defense of Democracies’ Schanzer, who worries that a lack of attention to Iran’s support of terrorism, and its links to al-Qaida, ultimately could give Iran an advantage in negotiations.

“This is a very dangerous regime that we’re playing with, and I don’t believe we’re playing on equal footing,” he said. “You have to really begin to wonder if Iran crosses that nuclear threshold, they’re able to get that nuclear weapon, they could put it in the hands not just of Hezbollah or Hamas but potentially into the hands of al-Qaida.”

But former congressman Hamilton, while concerned about the Iran-al-Qaida connection, plays down the danger.

“Nations do not usually share nuclear secrets very easily with anyone, and certainly with one they do not control,” Hamilton said. “The paramount interest of the United States now, of course, is to limit any possibility of a breakout toward a possible nuclear weapon in Iran," he said. “That is the focus of the diplomacy today and it seems to me, should be.”

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