Sombre ceremonies are taking place in New York, Washington and Pennsylvania at the sites of the suicide plane crashes that shook the world and led to a dramatic shift in American foreign policy.
However as the services got underway Osama bin Laden's number two Ayman al-Zawahiri warned that the Gulf and Israel would be the next targets of Al-Qaeda.
The cilling warning came in a video message coinciding with the fifth anniversary of the September 11 attacks on the United States.
"You should not concern yourself with the troops in Iraq and Afghanistan. They are already doomed," Zawahiri said in the message, according to extracts published on an Internet site.
"Instead you should worry about your presence in two areas. The first is the Gulf, from where you will be expelled. And the second is Israel."
Bush launches commemorations
US President George W. Bush launched the anniversary events in New York by laying wreaths in reflecting pools where the World Trade Center's twin towers once stood.
Accompanied by his wife Laura, Bush silently placed two garlands at the spot popularly known as "Ground Zero" before attending a service of prayer and remembrance at Saint Paul's Chapel across the street.
"And I vowed that I'm never going to forget the lessons of that day," he said. "There's still an enemy out there that would like to inflict the same kind of damage again."
Mr Bush has called for flags to fly at half-mast across the US and for people across the country to observe a moment of silence at 8:46 am (1246 GMT), the exact time that the first of two hijacked airliners ploughed into the World Trade Center.
Mr Bush will lay a wreath in the Pennsylvania field where a third jet crashed after passengers fought back against their hijackers, killing 40 people.
He will then fly to the US Defence Department's Pentagon headquarters for commemorations there.
In what has become an annual ritual, husbands, wives and partners of the 2,749 people who perished in the World Trade Center will read a roll call of the dead.
As evening falls, two giant beams of light symbolising the collapsed towers will illuminate the Manhattan sky. A candle-lit vigil is planned at Ground Zero.
Iraq and al-Qaeda
On the eve of the anniversary, US administration officials admitted that ousted Iraqi leader Saddam Hussein was not behind the al-Qaeda attacks on US targets but defended the decision to invade, insisting Saddam was linked to the network.
"We've never been able to confirm a connection between Iraq and 9/11," Vice President Dick Cheney said on NBC, but said that a connection with al-Qaeda was "different issue."
"There are two totally different propositions here. People have consistently tried to confuse them," he said, calling Saddam a state sponsor of terror and noting that al-Qaeda leader Abu Musab al-Zarqawi was in Iraq before the US invasion.
Despite the billions of dollars spent on the military campaigns, bin Laden, believed to be hiding in the rough, mountainous region straddling the Afghanistan-Pakistan border, remains at large, and the Washington Post has reported that his trail had grown "stone cold."
The newspaper, citing unnamed US and Pakistani officials, said no tips, human or electronic, had led them anywhere near the al-Qaeda leader.
Location 'unknown'
Secretary of State Condoleezza Rice acknowleged that the United States did not know bin Laden's precise location, noting that he is in "apparently, very remote areas."
"He doesn't communicate, apparently, very much," she said in an interview on Fox News. "And it is not easy to track someone who is determined to hide in very remote areas."
But, she said, there are "fewer and fewer places for him to hide."
However, Ms Rice said the US had "badly hurt" the al-Qaeda movement and the US was clearly a safer place than the day five years ago.
"I think it's clear that we are safer, but not really yet safe. We're more secure, our ports are more secure, our airports are more secure,” she said.
"We have a much stronger intelligence sharing operation, not just within the country where we've broken down walls between law enforcement and intelligence agencies to get all of the information to break up terrorist plots, but also across the world."
"We've clearly hurt badly the al-Qaeda organisation that planned and plotted and executed September 11, capturing many of their major field generals.”
She specifically referred to Khalid Sheikh Mohammed, the self-proclaimed architect of the September 11 attacks, and suspected bin Laden aide Abu Zubaydah who were moved last week from secret CIA custody to the US military prison at Guantanamo Bay, Cuba.