The State Department said that “Iran continues to deny al-Qaeda’s presence in the country, despite their knowledge of al-Qaeda leadership figures’ activities there," the relationship dating back to as early as 2009. 

This is clearly proof that Iran is trying to take "patronage" over all Muslims terror groups even the Sunni ones, as Hamas and Al-Qaeda are.

The State Department also confirmed remarks by James Rubin, the US special coordinator for the State Department’s Global Engagement Center, who recently talked of “a new partnership between Iran and al-Qaeda" in a briefing in London, saying that Iran is harboring al-Qaeda leaders inside its soil. 

The department also emphasized that “Iran is the leading state sponsor of terrorism, facilitating a wide range of terrorist activities and other illicit activities around the world -- in Bahrain, Iraq, Lebanon, Syria, and Yemen, through militant groups and terrorists such as Hezbollah and Hamas.”

They branded Iran "a primary driver of instability across the Middle East" since the Islamic regime was established in 1979.
Late in January, the United Nations released a report disclosing eight new al-Qaeda training camps and other infrastructure inside Afghanistan as well as five madrasas, or religious schools to teach jihadi ideology. An al-Qaeda leader known as Hakim al-Masri “is responsible for the training camps and conducting suicide bomber training for Tehrik-i-Taliban Pakistan,” the Pakistani branch of the outfit. Al Qaeda has also established a new base “to stockpile weaponry” in the central province of Panjshir. 

The report cited several UN Security Council member states as saying that the key al-Qaeda figures are travelling to provide liaison between the terrorist group’s de facto leader, Saif al-Adel, who resides in Iran, and senior al-Qaeda members in Afghanistan, including Abdul Rahman al-Ghamdi. Al-Ghamdi is one of the suspects in the September 11 attacks, who was unable to participate for unknown reasons.