Al Qaeda remains the single greatest threat to the United States, Hayden said in a speech to the Atlantic Council. "If there is a major strike on this country, it will bear the fingerprints of al Qaeda."
"All the threats we have to the West have a thread that takes it back to the (Afghanistan/Pakistan) border," Hayden added.
Hayden said there has been no spike in terrorist "chatter" to suggest an attack on the United States linked to the presidential transition.
"But we don't know what we don't know," he said.
He said the intelligence agencies have received "very clear direction" to make this the smoothest transition in history "so there is no diminution in the ability of the republic to defend itself." It is the first wartime transfer of power in 40 years.
Hayden said bin Laden, believed to be hiding in the lawless tribal border area of Pakistan, "appears to be largely isolated from the day-to-day operations of the organization he leads."
The hunt for bin Laden remains at the top of the CIA's priority list.
"His death or capture clearly would have a significant impact on the confidence of his followers both core al Qaeda and unaffiliated extremists throughout the world," Hayden said.
Al Qaeda-affiliated groups in the Philippines and Indonesia, Saudi Arabia and Iraq have been degraded, but al Qaeda cells are surfacing elsewhere, Hayden said.
"In East Africa, al Qaeda is engaging Somali extremists to revitalize operations," the CIA director said. "The recent bombings in Somalia may have been meant, at least in part, to strengthen bona fides with al Qaeda's senior leaders. A merger between al-Shabaab and al Qaeda could give Somali extremists much-needed funding, while al Qaeda could claim to be re-establishing its operations base in East Africa."
Recent attacks by an Algerian-based, al Qaeda-linked group known as Lands of the Islamic Maghreb are bigger and more deadly than at any time since the group merged with al Qaeda two years ago, he said.
Al Qaeda also is strengthening in Yemen with an "unprecedented number of attacks" in 2008 and is likely to be a launching pad for attacks against Saudi Arabia.
Additionally, al Qaeda's safe harbor in Pakistan has allowed it to train a "bench of skilled operatives" that can carry out attacks when other plans are disrupted, he said.
Iraq also remains a terrorist staging ground. Al Qaeda fighters seasoned in the Iraq war but now leaving for other countries pose a continuing concern, Hayden warned.