On Monday, he will also visit the Pentagon outside Washington and a farm field near Shanksville, Pennsylvania. With New York's fallen Twin Towers, the three locations mark the spots where four civilian airliners crashed with suicide hijackers aboard.
On Monday, the nation is to observe a moment of silence, and Bush will give a live address on national television.
With Congressional elections due November 7, Bush has built up to Monday's anniversary with a series of speeches hammering home his message that the US faces a long, historic struggle to defeat terrorism.
His commemorations of the worst terror attacks on US soil begin with a wreath-laying ceremony Sunday at the New York site where the World Trade Center's twin towers collapsed, after terrorists crashed jetliners into them on the morning of September 11, 2001.
From the place Americans call Ground Zero, Bush and his wife, Laura, will move across the street to a prayer service at St. Paul's Chapel in lower Manhattan.
On Monday, the actual anniversary of the attacks, Bush is due to have breakfast with New York rescue workers before observing a moment of silence at 8:46 am, the exact time the first plane struck the north tower.
He plans to visit the two other September 11-linked sites later Monday - the US Defence Department headquarters outside Washington, which was struck by the third plane, and a field in rural Pennsylvania where the fourth jetliner crashed apparently as passengers tried to storm the cockpit.
To cap the anniversary, Bush is to address the nation in a televised evening speech from the White House.
Nearly 3,000 people died in the September 11 attacks. This year's anniversary comes against the backdrop of the increasingly unpopular war in Iraq - the main reason why members of Bush's Republican Party face a tough battle to retain control of both houses of Congress in the November elections.
Taking on his critics in his speaking tour since last week, Bush has portrayed Iraq as the central battleground against al-Qaeda terrorists.
He has likened the US war on terrorism to earlier battles against Nazism and communism. Bush has evoked dramatic, previously unreleased details of how al-Qaeda operatives plotted the September 11 attacks and has assured Americans that the country is safer than it was five years ago.
A recent ABC television poll said that Bush's approval rating has risen to 42 per cent, back up from an all-time low of 33 per cent in May.
But a CNN poll this week found that 53 per cent of Americans do not view the Iraq war as part of the war on terrorism. Both polls had margins of error of plus or minus 3 percentage points.
At the former World Trade Center site, a temporary memorial museum opened last week. Work has also begun at the location on the striking Freedom Tower, designed to be the world's tallest building when completed in 2013.
Construction workers broke ground on the building in March after delays due to disputes over the design, concerns about security and bickering over the site's ownership. A full-fledged memorial museum is due to open in 2009.
Several temporary memorials have sprung up around the site near Wall Street in the historic heart of New York. A plaque on the south side commemorates the more than 300 firefighters who died coming to the rescue of people trapped inside the burning towers.
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