"Yes, this is what I wish, to be a martyr for a long time," Mohammed told the court. "I will, God willing, have this by you."
It was the first time that Mohammed had appeared before the outside world since his capture in 2003. He and four others accused of plotting the Sept. 11 attacks were held in secret CIA prisons until 2006, when they were transferred to Guantanamo Bay.
The five will face the death penalty if they are convicted of crimes including murder, conspiracy and terrorism.
At the arraignment, Mohammad was dressed in a clean white tunic and turban, according to the Associated Press -- a contrast to his disheveled appearance in a T-shirt when he was first captured nearly five years ago.
When the judge, Marine Col. Ralph Kohlmann, asked whether Mohammed was satisfied with the military lawyer assigned to him, Mohammed said that he would represent himself instead. He also began to chant in Arabic, translating his words as "There is no God but Him; in Him I have put my trust."
Officials in charge of the trial are prepared for many challenges from the defense, including whether evidence obtained from CIA interrogations that critics say included torture should be admissible in court. Mohammed was one of three al-Qaida suspects who underwent waterboarding, a technique the CIA says it no longer uses.
Prosecutors want to start the trial on Sept. 15. The trial will be a high-profile test of a military tribunal system that has been mired in controversy for years. It was established by President Bush after the Sept. 11 attacks, but ruled illegal by the Supreme Court in 2006. Congress later passed a new law allowing it to be reestablished.
"This is a fundamentally flawed process and we will zealously identify and expose each and every one of its flaws," chief defense counsel Col. Steven David said.
Journalists watched the proceedings on closed-circuit television in a nearby room, but no photographers were allowed to record the arraignment. The judge also announced that there would be a 20-second delay in order to stop the feed if any classified information were revealed, AP reported.