In Washington, President Bush paused for a moment of silence outside the White House, while at the Pentagon, Gen. Peter Pace spoke at the wall where the hijacked plane broke through.
Pace, chairman of the Joint Chiefs of Staff, told the victims' families that their loved ones will always be remembered.
"I do not know the proper words to tell you what's in my heart, what is in our hearts, what your fellow citizens are thinking today. We certainly hope that somehow these observances will help lessen your pain," he said.
Pace also spoke of the military, calling the anniversary "a day of recommitment." At the main U.S. base at Afghanistan, service members bowed their heads in memory of the victims.
National intelligence director Mike McConnell said U.S. authorities remain vigilant and concerned about "sleeper cells" of would-be terrorists inside the United States. "We're safer but we're not safe," McConnell said on ABC's "Good Morning America."
Even though the World Trade Center ceremony gathering was moved out of ground zero, an estimate 3,500 family members descended briefly into the site to lay flowers near the twin towers' footprints.
Among the first family members down the ramp was Marjorie Miller, whose late husband Joel worked at Marsh & McLennan. She said the rain was almost welcome after five consecutive years of Sept. 11 sunshine.
"A lot of tears coming down from up there," she said, gesturing toward the sky, "and a lot of tears down here."
In all, 2,974 victims were killed by the Sept. 11 attacks: 2,750 connected to the World Trade Center, 40 in Pennsylvania and 184 at the Pentagon. Those numbers do not include the 19 hijackers.
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The images, recorded by Pentagon security cameras outside the building, were made public in response to a December 2004 Freedom of Information Act request by Judicial Watch, a public interest group.
Military jets thundered through the sky above New York after a wreath-laying ceremony aboard an aircraft carrier turned into a museum.
District Judge Leonie Brinkema said the jury considering whether to execute Moussaoui could hear the recording from United Airlines Flight 93 and see a transcript of it.
Mayo was to appear in federal court later Thursday on a charge of interfering with a flight crew after disrupting United 923 as it flew from London to Washington, D.C., on Wednesday.