The men — which include alleged mastermind Khalid Sheikh Mohammed — are accused of planning the atrocities in which two planes crashed into the World Trade Center. All five are imprisoned in Guantanamo Bay.
They will face charges including terrorism, hijacking and conspiracy to murder at a military war crimes tribunal. US President Barack Obama had originally pledged they would be tried in a civilian court — and the change of heart has sparked criticism from civil rights groups.
The other four men are Waleed bin Attash, Ramzi Binalshibh, Ali Abd al-Aziz Ali and Mustafa Ahmad al-Hawsawi. The attacks, in which another plane was flown into the Pentagon and a fourth downed in a Pennsylvania field, resulted in the deaths of 2,976 people.
The suspects are to hear their charges read out in a military court within 30 days. They are being tried at a military tribunal following huge opposition to a hearing in a civilian court. It comes after Obama also had to go back on a pledge to shut down Guantanamo Bay.
Khalid Sheikh Mohammed has admitted responsibility for the attacks, the Pentagon has previously said.
Other terror acts
Mohammed, who was captured in Pakistan in 2003 and has been detained in Guantanamo since 2006, has said he intended to plead guilty.
Other terrorist activities he is alleged to have been involved in were the 2002 nightclub bombing in Bali, the murder of American journalist Daniel Pearl and a failed 2001 bid to blow up a plane with a shoe bomb.