"Our hearts still ache for the futures snatched away, the lives that might have been," Obama said.
The president also paid tribute to the four Americans killed one year ago in an attack on a U.S. compound in Benghazi, Libya, asking the country to pray for those who "serve in dangerous posts" even after more than a decade of war.
Obama opened the day with a moment of silence on the South Lawn of the White House.
Along with first lady Michelle Obama the president walked out of the White House at 1246 GMT the moment on Sept. 11, 2001, when the first plane hit the World Trade Center tower in New York City. Obama and the others assembled bowed their heads for a moment, and then listened as a bugler played "Taps."
Nearly 3,000 people were killed in the attacks that led to a long war in Afghanistan.
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