Yes, Shia Iran works with Sunni Al Qaeda. I documented this for CBN News way back in February '09 and highlighted it again last month on the first episode of my new show, Stakelbeck on Terror (7:25 into the show). Here's more, from the Wall Street Journal:
Cooperation among Iran, al Qaeda and other Sunni extremist groups is more extensive than previously known to the public, according to details buried in the tens of thousands of military intelligence documents released by an independent group Sunday.
U.S. officials and Middle East analysts said some of the most explosive information contained in the WikiLeaks documents detail Iran's alleged ties to the Taliban and al Qaeda, and the facilitating role Tehran may have played in providing arms from sources as varied as North Korea and Algeria.
The officials have for years received reports of Iran smuggling arms to the Taliban. The WikiLeaks documents, however, appear to give new evidence of direct contacts between Iranian officials and the Taliban's and al Qaeda's senior leadership. It also outlines Iran's alleged role in brokering arms deals between North Korea and Pakistan-based militants, particularly militant leader Gulbuddin Hekmatyar and al Qaeda.
WikiLeaks released a cache of intelligence documents Sunday that detail raw intelligence reports over a five-year period. The information is fragmentary, and its not known how many reports were corroborated by other sources. "Some parts are more believable than others, but this sort of raw stuff could be gold or a dud," said a senior U.S. official working on both Pakistan and Iran.
The apparent links are striking because Iran has historically been a foe of the Taliban, who generally view the followers of Shiite Islam—Iran's predominant faith—as heretics.
No matter. As my friend Ken Timmerman has said many times, when it comes to killing Christians and Jews, Sunni and Shia jihadists get along just fine.