Americans stood in silence as ceremonies were held at the sites in New York, Washington and Pennsylvania where hijackers crashed four airliners killing 3,000 people.
George Bush and his wife, Laura, bowed their heads for two moments of silence at New York's Fort Pitt firehouse - the first the moment a plane flew into the north tower and then when the south tower was hit.
At the site - where the 110-storey twin towers stood until five years ago - New York police and firefighters gathered on the lowest level of the site for a flag-waving ceremony. Families carrying bouquets of roses stood around two small reflecting pools that marked where the two towers once stood.
Relatives and partners of victims took nearly four hours to read out the names of all 2,749 people who died at the World Trade Centre.
Felicia Cappo, who lost a brother in the south tower, said: "It's hard to believe that it's been five years. It's always going to seem like yesterday."
United Flight 93
Bush also visited Shanksville, Pennsylvania, for a wreath-laying ceremony in the countryside where United Flight 93 crashed into the ground after passengers tried to take control of the airliner from the hijackers. Forty passengers and crew were killed.
Later, the president will attend a ceremony at the Pentagon where 184 people died and make an address to the nation.
Bush attended a service at the
crash site of flight United 93
Kofi Annan, the United Nations secretary-general, said the attacks inflicted a "gaping wound" on New York and reminded the world that terrorism was unacceptable, no matter who commits it.
"The attacks of September 11, 2001, cut us all to the core, for they were an attack on humanity itself," Annan said in a statement as the 191-member General Assembly and 15-nation Security Council observed a minute of silence.
The anniversary focused the debate ahead of November's elections on how best to protect Americans from future attacks and intensified criticism over the unpopular war in Iraq.
Hillary Clinton, New York Democratic senator, told CBS' 'Early Show': "We took our eye off the ball.
"I mean, we diverted resources and attention to Iraq and we didn't finish the job."
Facing the prospect that Democrats could take control of the US Congress from his fellow Republicans in the November election, Bush and his cabinet have been pushing their record on national security as they did during Bush's 2004 re-election campaign.
Dick Cheney, the US vice-president, called September 11 "a day of national unity," and used the remembrance ceremonies to highlight the necessity of the ongoing "war on terror".
He said: "We have no intention of ignoring or appeasing history's latest gang of fanatics trying to murder their way to power."
The United States was on high alert during the remembrance ceremonies. Pennsylvania Station in New York was briefly evacuated when a suspicious bag was found and a United Airlines flight from Atlanta to San Francisco was diverted to Dallas because of an unclaimed BlackBerry email device.