Clarke said that while Zawahiri's threats in recent years have been largely empty, "the question remains is al Qaeda planning a major attack during the transition or early in the Obama administration."
The message comes after two months of silence from Zawahiri and just days after Obama's announcement that his administration will go after al Qaeda and renew efforts to capture Osama bin Laden. It is the first al Qaeda propaganda message to get out in four months.
"It's all part of the big plan to confront them, to confront them on every level," said former CIA officer and ABC News Consultant John Kiriakou.
As for bin Laden, the CIA believes he is still alive and hiding in Pakistan, where he is thought to be under siege and facing the greatest threat to his safety in years.
"Because they feel under siege and because the United States is going through a transition," said Clarke, "we are at a greater risk of attack than in some time."