In New York, relatives are reading out the names of those killed when hijacked jets were crashed at the World Trade Center, Washington and Pennsylvania.
Barack Obama laid a wreath at the Pentagon and Vice-President Joe Biden is expected to speak at Shanksville.
For the first time, politicians will not address the ceremony in New York.
At the Pentagon, Barack Obama addressed survivors of the attacks and relatives of those killed. He told them their loved ones would never be forgotten, and that the dead had “helped us make the America we are today”.
“The true legacy of 9/11 will not be one of fear or hate or division,” Barack Obama said.
“It will be a safer world, a stronger nation, and a people more united than ever before.”
The National September 11 Memorial and Museum announced in July that this year’s ceremony at Ground Zero would include only relatives reading victims’ names.
Memorial President Joe Daniels said that, in an election year, it was “honoring the victims and their families in a way free of politics”.
Charles Wolf, whose wife Katherine was killed at the World Trade Center, said the absence of elected officials would make the event more intimate for the families.
“We’ve gone past that deep, collective public grief,” he said.
Tuesday dawned with a clear blue sky over Washington and New York, jogging memories of a similar September morning 11 years ago.
Nearly 3,000 people were killed that day in attacks by al-Qaeda members who had hijacked four airliners.
President Barack Obama and First Lady Michelle Obama observed a moment of silence at the White House at 08:45.
They then headed to the Pentagon to attend a memorial ceremony there, where one of the jets crashed, and then visit wounded soldiers at Walter Reed Army Medical Center.
With a US election looming in November, President Obama and his Republican rival Mitt Romney have set aside campaigning for the day and will not run negative advertisements.
Mitt Romney was due to visit Reno, Nevada, to address a National Guard unit whose members were deployed as part of the US response to the attacks.
“On this most sombre day, those who would attack us should know that we are united, one nation under God, in our determination to stop them and to stand tall for peace and freedom at home and across the world,” Mitt Romney said in a written statement.
Vice-President Joe Biden and Secretary of the Interior Ken Salazar were due to speak at the Flight 93 National Memorial, near Shanksville, where one of the jets crashed as passengers attempted to overpower the hijackers.
A 9/11 museum in New York was due to have been completed for the 11th anniversary but has been plagued by setbacks.
Officials say it will take at least another year to finish.
A new building – the $3.9 billion One World Trade Center – is due to open in 2014 on the north-west corner of Ground Zero.
Last year an outdoor memorial was opened at the site and has since been visited by almost 4.5 million people.
In the aftermath of the 2001 attacks, the US launched a campaign to destroy the al-Qaeda network headed by Osama Bin Laden.
A team of elite US troops killed the al-Qaeda chief in a raid on his Pakistani compound last year.
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