The U.S. Treasury Department yesterday announced sanctions on six al-Qaeda leaders who have used Iranian territory to funnel money and recruits to al-Qaeda’s core leadership in Pakistan and to its bases in Afghanistan and Iraq. Treasury officials say the al-Qaeda leaders have been operating in and through Iran with the acquiescence of that government since 2005.

Iran had detained several senior al-Qaeda operatives who fled there after the U.S.-led invasion of Afghanistan in 2001, keeping them under house arrest for several years. In 2009, however, Iran released Osama bin Laden’s son, Saad bin Laden. More recently, Iran has allowed al-Qaeda operatives, including top military strategist Saif al-Adel, to operate freely from its territory.

There is ongoing debate within the U.S. government about the extent to which Iran helps al-Qaeda. Al-Qaeda has denounced Shi’ism, the sect of Islam to which Iranians adhere that forms the basis of legitimacy for the theocratic regime in Iran. In fact, al-Qaeda in Iraq was responsible for targeting and killing thousands of Iraqi Shia, including Iranian-backed Shia militias. Additionally, al-Qaeda operatives in the Kurram Agency of Pakistan’s tribal areas have been accused of fomenting Shia–Sunni violence there in an effort to weaken Shia dominance in the area.

Iranian leaders would likely take a somewhat cautious approach in their support for al-Qaeda. While they would support al-Qaeda’s attacks on U.S. interests in the region, they would want to avoid being too closely associated with the anti-Shia organization.

Publicly criticizing Iran for harboring al-Qaeda leaders comes with little cost to U.S. policy, since there is no American diplomatic presence in Iran. U.S. accusations against Pakistan (where al-Qaeda’s core leadership has sheltered for nine years) carry a higher diplomatic cost, since the U.S. relies on a substantial intelligence presence in that country to track terrorists and crucial transportation lines that resupply coalition troops in Afghanistan.

When it comes to degrading al-Qaeda’s capabilities, Pakistan is still the biggest challenge for U.S. policymakers. Departing chief of the CIA National Counterterrorism Center Michael Leiter said recently that “Pakistan remains a huge problem” and that “the core organization is still there.”

U.S. officials often mention Iran as one of the key players in reaching a regional settlement in the Afghan conflict. Tehran maintains significant influence with Afghan leaders in western Afghanistan, which borders Iran. But the U.S. can hardly condone a diplomatic role for Iran in resolving the Afghan conflict if it persists in its support for al-Qaeda’s activities in the region.