The CIA equally is interested in those jockeying to replace bin Laden in what he predicted will be a "succession crisis."
"It will be really interesting to see how that plays out. The organization is a lot more networked than it is ruthlessly hierarchical," Hayden said of the group behind the Sept. 11, 2001, attacks on the United States. "How do you pick the next overall leader?"
A number of Egyptians are now part of al Qaeda's top echelon and may struggle for power among themselves. Bin Laden's current No. 2, Ayman al-Zawahri, is an Egyptian.
Despite al Qaeda's resilience, taking out bin Laden would be a psychological blow to the organization, Hayden said.
"If there ever was a sense of invulnerability, I think killing or capturing him would shatter it once and for all," he said.
Bin Laden is believed to be hiding in the lawless tribal areas of western Pakistan. The new Pakistani government is negotiating a new peace agreement with the area's tribal leaders that would have them expel extremists and police the region on their own. Hayden said he believes the result will be similar to the last agreement Pakistan struck with the tribes, which changed nothing.
"Any peace agreement that does not move the effective writ of the Pakistani government into the tribal region and push the rule of law there gives these groups the opportunity to continue to train, refit and move across the Afghan border. It's something we certainly could not look kindly on," Hayden said in the telephone interview.
The CIA has been using armed drones to attack alleged terrorists inside the tribal area, as U.S. military forces are barred from pursuing al Qaeda and Taliban fighters across the Afghan border.
Hayden would not say what else the CIA is doing, if anything, to target terrorist enclaves there.
"It's hard for me to get into any details. I understand the situation there, and I'm comfortable with the authorities we've been given," he said.
"There's an awful lot of senior leadership killed or captured including even in the last several months," he said.
Although bin Laden remains at large, Hayden said, "On balance I think we are doing pretty well on the war on terror."
"It's not luck," he said. "We've made it more difficult for people who would do us harm. That's not a guarantee. It doesn't mean they won't be back. It doesn't mean we'll always be successful."
One tactic that has caused worry is the CIA's holding of prisoners outside the reach of the International Committee of the Red Cross. The CIA has held fewer than 100 prisoners but kept some of them for years. That program was born of the decision shortly after the Sept. 11 attacks to put the CIA in charge of interrogations of alleged terrorists. The CIA also has come under criticism for harsh interrogation practices, including waterboarding, which gives the victim the sensation of drowning.
"We were kind of turning into the nation's jailer, a wholly inappropriate role for us," Hayden said.
The CIA is still holding prisoners but for less time. It recently turned over two detainees to the U.S. military at Guantanamo Bay Naval Base after a few months.
"I'm not uncomfortable with the interrogation part or the detention required to conduct the interrogation. But once the intelligence value is bought off to a certain point, we have to move on," he said.
Hayden said he authorizes only intelligence activities that meet several tests, including whether the activity can withstand political shifts.
"We can't stand an American counterterrorism program with an on-off switch every other November," he said, referring to the American election cycle.
On other topics, Hayden said:
-Iran's intention is to produce its own nuclear fuel, using Iranian technology.
"That gives them the potential at any moment to break out and create a weapon, and that's what of course is most troubling."
-Even without Israeli intelligence, the CIA would have known by last July that a building in Syria's western desert was meant to be a secret nuclear reactor when a pipe system from the Euphrates River to the building was constructed.
"That was a powerful cooling system going to a building with no visible heat source," Hayden said. Israeli jets destroyed the building in August 2007, although Syria has denied it was a nuclear facility.
-North Korea's arms trade - helping Syria build a nuclear reactor or selling missile technology to Iran - is motivated by cash. "It's a starved economy, with very, very few sources of foreign exchange," he said. "This is one of the ones where they can actually turn a profit."