The US is marking nine years since 9/11 amid controversy over plans for an Islamic centre near Ground Zero and a threat to burn the Koran.
In New York, relatives read out the names of those who died when hijacked airliners hit the World Trade Center.
At the Pentagon, also hit by a hijacked plane on 9/11, President Barack Obama said the US was not at war with Islam.
Later on Saturday, rival protests began close to Ground Zero, by groups opposed to or supporting the building of a controversial Islamic cultural centre in the area.
'Deeply cut'Speaking at a memorial event at the Pentagon, President Obama paid tribute to those who died on 11 September 2001.
He said that while it was tempting to dwell on their final moments, the memorial events were taking place "to remember the fullness of their time on Earth".
Mr Obama also repeated his recent calls for unity, saying: "It was not a religion that attacked us that September day. It was al-Qaeda".
"We will not sacrifice the liberties we cherish or hunker down behind walls of suspicion and mistrust".
BBC News
