Donald Trump delivered a speech commemorating the airplane passengers who are thought to have charged the cockpit to stop the attackers.
Ceremonies are also being held at NYC’s 9/11 Memorial plaza on the World Trade Center site.
2,996 people were killed in the deadliest foreign attack ever on US soil.
President Trump said in Shanksville on September 11: “America’s future is not written by our enemies. America’s future is written by our heroes.
“As long as this monument stands, as long as this memorial endures, brave patriots will rise up in America’s hours of need and they, too, will fight back.”
He spoke at the newly inaugurated Tower of Voices memorial, a 93ft tall structure with 40 wind chimes.
On September 11, 2001, hijackers flew planes into the World Trade Center in New York City, and the Pentagon in Arlington, Virginia.
Another plane, United Airlines Flight 93, crashed in a field in Shanksville, Pennsylvania.
It is believed hijackers were planning to aim that aircraft at the Congress or White House in Washington DC before it went down, killing all 40 people aboard.
Cockpit voice recordings of the hijackers and mobile phone calls from those aboard to loved ones indicate passengers tried to fight their way into the cockpit to regain control before the plotters nosedived the plane.
President Trump praised the passengers’ “incredible valor” and said their revolt was “the moment America fought back”.
He said: “A band of brave patriots turned the tide on our nation’s enemies and joined the immortal rank of American heroes.”
Donald Trump is the third sitting president to attend the crash site, 70 miles south-east of Pittsburgh.
Senator John Cornyn, a Texas Republican, was among those who noted this is the first year that Americans born after the attacks will be old enough to enlist in the US military.
During remarks at the Pentagon, VP Mike Pence told audience members they “must learn the lessons of 9/11 and remain ever vigilant”.
The ceremony in New York was attended by New York Governor Andrew Cuomo, US ambassador to the United Nations Nikki Haley and Mayor Bill de Blasio, as well as former mayors Michael Bloomberg and Rudy Giuliani.
Relatives of victims read out the names of the dead, and moments of silence were observed at 08:46 and 09:03 to mark the times when passenger jets struck the two skyscrapers.
In the years since the attacks, cancer cases in lower Manhattan – especially among first responders who dug through the toxic rubble – have increased.
The 9/11 Victims’ Compensation Fund has paid out $4 billion to fund medical expenses for survivors of the terror attacks.
According to the World Trade Center Health Program, nearly 10,000 of them have had some form of cancer.
Tens of thousands of people inhaled fumes in the days after the attack, and the number of patients coming forward with tumors has increased in recent years, according to the fund.
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