Yemeni Ali Hamza al-Bahlul, who has acknowledged that he is "from al-Qaida", is one of only nine Guantanamo prisoners charged with crimes.
A separate tribunal also began on Wednesday for Omar Khadr, a 19-year-old Canadian who is accused of killing a US army medic in Afghanistan when he was 15.
Meanwhile, Aljazeera reports quoting Major Jeff Wayne, the prison camp's deputy director of public relations, that 40 Guantanamo detainees continue to be on hunger strike. However, he denied the latest allegations of torture levelled by Amnesty International.
Most of the 500 or so detainees at Guantanamo have been held without charges for years. The pre-trial hearings at the remote military base in Cuba began on the fourth anniversary of the opening of Guantanamo as a prison for terrorism suspects.
Al-Bahlul is accused of conspiring to commit war crimes by acting as a bodyguard for bin Ladin and making recruiting videos for al-Qaida.
He said he did not recognise the authority of what he called an illegal tribunal set up by enemies of the Muslim nations.
"There's going to be a tribunal of God on the day of judgment," al-Bahlul told the court in Arabic. "Do what you have to do and rule however you have to rule ... God will rule based on justice."
Khadr, 19, is accused of killing a
US army medic in Afghanistan
Al-Bahlul ended his participation in the proceedings with one word in English, "Boycott", and the presiding officer, army Colonel Peter Brownback, set his trial tentatively for 15 May.
The tribunal for Khadr, accused of killing the medic with a grenade during a firefight at a suspected al-Qaida compound in Afghanistan, was less colourful.
Khadr quietly answered "Yes sir" when the presiding officer, Marine Colonel Robert Chester, asked him if he understood his rights. He reserved the right to enter a plea later.
Khadr wore khaki pants and a blue-and-red T-shirt with the huge logo of the Canadian sportswear firm Roots.
Chester said the attire violated court rules and urged the lawyers to find Khadr an appropriate shirt before his hearing resumed on Thursday at 1pm.
Through his military lawyer, Captain John Merriam, Khadr asked that a more experienced military attorney be appointed to represent him.
Up to 40 detainees are on hunger
strike in Guantanamo prison
The hearing was the first time that Merriam has defended anybody in a courtroom, and Chester said he thought the request could be granted.
The Pentagon is proceeding with the two cases even though courts have halted the trials of other Guantanamo prisoners pending a US Supreme Court ruling on whether George Bush as president had authority to establish the tribunals to try foreign terrorism suspects after the 11 September 2001 attacks.
The high court will hear arguments in the case in March.
Neither defendant was shackled or handcuffed in the courtroom. Both face life in prison if convicted.
Al-Bahlul read a list of nine reasons why he refused to be represented by a military lawyer or to participate further, including the treatment of Palestinians by Israel - "your allies, the Jews", he said.
Al-Bahlul also said Guantanamo prisoners had been tortured and that the Britons there had been released without being subjected to military tribunals.
He objected to the potential use of secret evidence and to the US characterisation of prisoners as illegal belligerents.
"We are prisoners of war and legal combatants based on our religion and our religious law"
Ali Hamza al-Bahlul,
alleged Bin Ladin bodyguard
"We are prisoners of war and legal combatants based on our religion and our religious law," he said.
Brownback rejected al-Bahlul's request to represent himself and al-Bahlul refused to meet Army Reserve Major Tom Fleener, the lawyer appointed by the military to defend him.
Smiling and thanking Brownback, al-Bahlul held up a sheet of paper scrawled with the word "Boycott" in English and Arabic.
He removed translation earphones, and refused to enter a plea or to stand when the charges were read.
Al-Bahlul's hearing ended on Wednesday. Khadr's will resume on Thursday to address defence complaints that the chief prosecutor made pre-judicial statements by telling journalists that Khadr was a terrorist whose family spent holidays with bin Ladin and trained to make bombs to kill Americans.