Confessed mastermind Khalid Sheikh Mohammed and the four other accused opted to plead neither innocent nor guilty, but rather to defer their plea to a later date, in the proceedings at the US naval base at Guantanamo Bay, Cuba.
The five face the death penalty if convicted for their roles in the 9/11 strikes by Al-Qaeda militants, which killed 2,976 people in New York, Washington and Shanksville, Pennsylvania.
The defendants were charged with "conspiracy, attacking civilians, murder and violation of the law of war, destruction, hijacking and terrorism" in connection with the attacks, the most lethal on US soil in modern history.
Mohammed, 47, was charged along with his Pakistani nephew Ali Abd al-Aziz Ali, also known as Ammar al-Baluchi; Mustapha al-Hawsawi of Saudi Arabia; and Yemenis Ramzi Binalshibh and Walid bin Attash.
After defying the court for more than nine hours by keeping silent, Mohammed and the co-defendants -- in a much-anticipated first public appearance in three years -- finally deferred their pleas.
"Maybe you're not going to see us any more," Binalshibh shouted out in a dramatic moment at the arraignment hearing, telling Judge James Pohl, "You are going to kill us."
Dressed in white jumpsuits, with some wearing white turbans, the men mostly refused to engage with the court officials -- reading what looked to be the Koran, keeping their eyes fixed on the ground, or kneeling to pray.
The defendants also passed a copy of The Economist magazine among themselves.
"Accused refused to answer," Pohl repeated over and over again.
At one point, Binalshibh suddenly stood to pray, interrupting the hearing.
He also shouted out: "The era of Kadhafi is over but you have Kadhafi in the camp ... you are going to kill us and say that we are committing suicide," referring to the slain former Libyan strongman.
Only one, bin Attash, was handcuffed when the group was brought into court, but Pohl ordered the cuffs removed after being assured he would "behave appropriately."
The arraignment, one of the last steps before a so-called "trial of the century" can take place, marks the second time the United States has tried to prosecute the 9/11 suspects.
Mohammed remained calm, his long, flowing beard appearing to have been dyed with red henna.
His lawyer David Nevin said his client, who three years ago confessed to the 9/11 attacks "from A to Z," probably would not speak at the hearing because he is "deeply concerned by the fairness of the process."
The accused men also refused to wear headphones to hear the simultaneous translation of the proceedings, which were being held in English. Their lawyers said it reminded them of their harsh interrogations.
Bin Attash's civilian attorney Cheryl Borman, the only woman on the defense team, was dressed in black and wore a hijab. "Because of what happened to them ... during the last eight years, these men have been mistreated," she argued.
Ten journalists and a similar number of victims' relatives attended the hearing, but heard the proceedings with a 40-second delay, in case sensitive information needed to be censored.
Dozens of other reporters watched on closed-circuit television.
The hearing comes about one year after President Barack Obama ordered the US Navy SEALs raid that killed Al-Qaeda chief Osama bin Laden.
The five men have been held for years at the US naval base in southeastern Cuba while a legal and political battle has played out over how and where to prosecute them. Debates have also raged over their treatment.
Mohammed was arrested in 2003 and spent three years in secret CIA jails where he was subjected to harsh interrogation techniques including waterboarding, which rights groups denounce as torture. He confessed to a series of attacks and plots.
The executive director of the American Civil Liberties Union, Anthony Romero, who was in Cuba to attend the hearings, called the military tribunal system "substandard" and "created to provide second-tier justice."
The Pentagon opened four military bases in the United States to allow families of the 9/11 victims to watch the case unfold on a giant screen.
The trial however is not likely to begin for at least another year.