Two moments of silence have been held in New York at the exact time 14 years ago that the two planes struck the towers of the World Trade Center.
Families of victims of the 2001 and 1993 World Trade Center attacks read out their names at Ground Zero, where the towers fell.
The attacks killed nearly 3,000 people, including more than 2,700 in New York.
A flag was raised at a ceremony at the Pentagon in Virginia, where a third plane crashed, killing 184 people.
In Shanksville, Pennsylvania, where a fourth plane crashed, Secretary of Homeland Security Jeh Johnson said passengers on United Airlines flight 93 "most likely saved hundreds or thousands of lives by losing their own."
At Ground Zero, Nereida Valle carried a photo of her daughter, Nereida DeJesus, who was 31 and working on the 98th floor of the south tower when she died.
"I feel her every day," she said.
The American flag flew at half-staff over the White House, where President Obama and First Lady Michelle Obama held a moment of silence on the South Lawn.
Vice President Joe Biden delivered remarks at a memorial event in New York along with New York Governor Andrew Cuomo and American singer Billy Joel.
He arrived at the event smiling and hugging people.
"People don't understand anniversaries are bittersweet, it all comes back," he said.
The president met members of the armed forces at Fort Meade in Maryland and had a long discussion including discussing where he was during the attacks.
His daughter Sasha had just been born and his older daughter Malia was starting school for the year.
"It gave you a sense for the first time, in my lifetime, that our homeland could be vulnerable," Mr Obama said. "We hadn't seen an attack like that since Pearl Harbor."
Mr Obama was a state senator in Illinois on 11 September 2001.
He heard reports on the radio while in the car on the way to a meeting in downtown Chicago and did not know how serious it was until he arrived.
"We have to remember how precious what we have is and defend it at any cost," he said.
He gave a nod to the first responders who were there on 9/11 and are still working today and said they are a "good reminder of the essential spirit of the American people."