A second defendant, Wallid bin Attash, also rejected his lawyers.
"I am a Muslim and I reject this session. The lawyers will stay here and be available to help me if I need, but I will represent myself," bin Attash said.
Al Jazeera's Mohammed Alami, who watched the hearings, said the judge granted Mohammed and bin Attash's wishes to represent themselves but expressed concern that they did not understand the dangerous and severe nature of the charges.
The September 11 attacks in 2001 killed
about 3,000 people
The other three defendants are Ramzi Binalshibh, Ali Abd al-Aziz Ali and Mustapha al-Hawasawi.
All five sat at defence tables alongside their lawyers, before Colonel Ralph Kohlmann, the judge, at the tribunal.
The defendants, whom authorities said had attended court willingly, wore cream-coloured clothing and turbans, without handcuffs.
Mohammed, seeming thin and with a thick grey beard and glasses, at times sang verses from the Quran in court until the judge told him to stop.
All five face trial in September, but some defence lawyers have argued this date does not give them enough time to prepare for trial and say the timing - two months before the US presidential election, is politically motivated to assist John McCain, the presumptive Republican candidate.
Journalists watched proceedings on close-circuit television in a nearby press room, while some observers were allowed into the courthouse.
The charges are the first to be brought against Guantanamo detainees over the September 11 attacks.
The US claims Mohammed confessed to masterminding the attacks and to involvement in about 30 other plots, but his lawyers say the confession was extracted by torture.
The CIA acknowledged earlier this year that Mohammed had been interrogated using the controversial "waterboarding" technique which simulates drowning.
He has been charged with 2,973 counts of murder over the death of each victim of the attacks in New York City, Washington DC and Pennsylvania.
The five men were transferred to the Guantanamo Bay prison in Cuba in September 2006 after reportedly spending about three years in secret CIA prisons.
Thursday's arraignment poses the most high-profile test so far to the US military tribunal system, which faces an uncertain future.
In 2006 the US Supreme Court struck down an earlier system as unconstitutional and it is to rule this month on the rights of Guantanamo prisoners, potentially delaying or halting the proceedings.
Eugene Fidell from the National Institute for Military Justice told Al Jazeera that while the creators of the military tribunals say they are better than international tribunals, they are not as good as US civilian courts or even the US military justice system, used for internal discipline.
And whether the outcome and conduct of the trials will satisfy people in the US or people overseas is still very much up in the air, he says.
Bush has less than eight months remaining in office and presidential candidates Barack Obama and McCain both say they want to close the military's offshore detention centre.
Source: Al Jazeera and agencies