"The Iranian regime kept some of these elements under house arrest," he said in an email to The Associated Press. "Some probably operate covertly. AQ members often transit Iran traveling between hideouts in Pakistan and Iraq."
U.S. intelligence officials have long tracked limited Al Qaeda activity inside Iran. Remnants of Al Qaeda's so-called management council are still there, though they are usually kept under virtual house arrest by an Iranian regime suspicious of the Sunni-/Salafi-based militant movement. There are also a small number of financiers and facilitators who help move money, and sometimes weapons and people throughout the region from their base in Iran.
Last fall, the Obama administration offered up to $12 million in rewards for information leading to the capture of two Al Qaeda leaders based in Iran. The U.S. State Department described them as key facilitators in sending extremists to Iraq and Afghanistan. The U.S. Treasury Department also announced financial penalties against one of the men.