During his trip to New York last week for the UN General Assembly, Ahmadinejad claimed in an interview with The Associated Press that explosive material and not planes brought down the World Trade Center.
He stopped short of saying the United States staged the disaster, but said that as an engineer, he's sure New York's twin towers were not brought down by jetliners.
"A few airplanes without previous coordination known to the security forces and the intelligence community in the United States cannot become missiles and target the heart of the United States," Ahmadinejad said.
In an article posted online in the terror network's English-language Internet magazine "Inspire," al-Qaeda rejected the Iranian leader's suggestions.
"Why would Iran ascribe to such a ridiculous belief that stands in the face of all logic and evidence?" asked the article's author, Abu Suhail. He said Iran wanted to portray itself as a country that stands up to the US.
"For Iran, anti-Americanism is merely a game of politics. It is anti-American when its suits it and it is a collaborator with the US when it suits it," Abu Suhail said.
He cited a number of examples of when Iran allegedly cooperated with the US, including in the invasion of Afghanistan.
Abu Suhail said Iran is jealous of al-Qaeda's "success" in the September 11 attacks, saying that because Tehran couldn't strike at the US itself, the Iranians want to "to discredit September 11 and what better way to do so than conspiracy theories."