Bin al-Shibh appeared to lead the group twice in prayer in the courtroom, once delaying the resumption of the hearing.
Mohammed, whose long beard appeared to be dyed red by henna, was much thinner than the last time he was seen publicly in a courtroom.
The judge, Col. James Pohl, needed the five to vocally confirm their desire to be represented by the attorneys who accompanied them to court. Because the defendants refused to cooperate, Pohl ruled the men would continue to be represented by their current military and civilian attorneys.
All five men are charged with terrorism, hijacking aircraft, conspiracy, murder in violation of the law of war, attacking civilians, attacking civilian objects, intentionally causing serious bodily injury and destruction of property in violation of the law of war.
If convicted, they face the death penalty.
There were so many allegations behind the charges, it took more than two hours for officers of the court just to read into the record the details of the 9/11 hijackings.
The reading of the charges "provided a stirring reminder of the importance of the case," Martins said Sunday.
"For so many people involved in this trial, the pursuit of justice is worth every moment spent," he said.
The next hearing is scheduled for June 12. It will likely be at least a year before the case goes to trial, Pohl said.
The charges allege that the five are "responsible for the planning and execution of the attacks of Sept. 11, 2001, in New York, Washington, D.C., and Shanksville, Pa., resulting in the killing of 2,976 people," the Defense Department said.
Though Mohammed confessed to organizing the September 11 attacks on New York and Washington, his confession could be called into question during a trial. A 2005 Justice Department memo -- released by the Obama administration -- revealed he had been waterboarded 183 times in March 2003. The technique, which simulates drowning, has been called torture by President Barack Obama and others.
The military initially charged Mohammed in 2008, but Obama stopped the case as part of his effort to close the U.S. detention center at Guantanamo Bay. Unable to close the center, Obama attempted to move the case to federal court in New York in 2009, only to run into a political firestorm.
The plan was dropped after complaints about cost and security, and Attorney General Eric Holder announced in April 2011 that the five would face a military trial at Guantanamo Bay. The decision was met with some criticism, including from the American Civil Liberties Union.
ACLU Executive Director Anthony D. Romero said last month that the administration is making a "terrible mistake by prosecuting the most important terrorism trials of our time in a second-tier system of justice."