Abd al-Rahim al-Nashiri says he confessed under torture
US military prosecutors have filed charges against the alleged mastermind of the 2000 attack on the USS Cole warship that left 17 sailors dead.
Saudi-born Abd al-Rahim al-Nashiri, who is being held at Guantanamo Bay, faces charges including murder and terrorism.
Mr Nashiri was arrested in the United Arab Emirates (UAE) in October 2002 and has been held at Guantanamo since 2006.
He told a hearing at the US base in Cuba last year that he confessed to the attack because he had been tortured.
Earlier this year, CIA director Michael Hayden acknowledged that the agency had subjected three suspects, including Mr Nashiri, to water-boarding - an interrogation technique which the CIA banned in 2006 and which human rights groups consider to be torture.
According to US intelligence, Mr Nashiri was the leader of the al-Qaeda network's operations in the Gulf.
The charges announced on Monday also allege involvement in other attacks, including one on a French supertanker in 2002.
Seventeen soldiers died in the USS Cole attack off Yemen
Brig Gen Thomas W Hartmann, legal adviser to the US military tribunal system set up at Guantanamo Bay, told reporters Mr Nashiri was charged with "organising and directing those attacks".
The Pentagon has said it will press for the death penalty in Mr Nashiri's case.
The BBC's Kevin Connolly in Washington says the military prosecutors have some significant hurdles to overcome in this case and others like it, however.
The trial will bring into sharp focus many of the legal and moral doubts which continue to swirl around the Guantanamo Bay prison camp and the military tribunals the US has created to deal with the prisoners it calls enemy combatants, our correspondent says.
It is not yet clear whether evidence gathered using such techniques as water-boarding will be regarded as admissible in court, or whether the prosecutors will present evidence that does not rely on the physical coercion of detainees.
The case will also raise another equally sensitive legal issue, our correspondent says.
The US Supreme Court recently ruled that Guantanamo inmates have the right to challenge the basis of their detention before American civil courts, prompting speculation that the Pentagon might wait for the outcome of those hearings before proceeding.
The announcement that it is to go ahead with Mr Nashiri's prosecution shows there will be no such delay, our correspondent concludes, suggesting that military tribunals will go ahead in parallel with civil proceedings seeking to have them declared unlawful.
In 2004, a Yemeni court tried Mr Nashiri in absentia over the USS Cole attack and sentenced him to death.