Louai al-Sakka is charged with masterminding and securing finance for the bombings of synagogues, the British consulate and an HSBC bank branch in November 2003. A Turkish al-Qaida cell claimed responsibility for the attacks.
Seventy people are already on trial in connection with the bombings.
At Monday's hearing, dozens of police kept tight security outside the courtroom. The judge ordered al-Sakka to leave the court after he refused to stand to make his defence.
"It is against my beliefs to stand for people like you," CNN Turk quoted al-Sakka as saying. "I carried out jihad. I killed Americans. Am I going to stand up for people like you?" he shouted as he was taken out of the courtroom.
The court also banned al-Sakka's lawyer Osman Karahan from representing his client as he has been charged with aiding and abetting al-Qaida.
Security sources have said al-Sakka, a bomb-making expert, was the top figure in Osama bin Laden's al-Qaida network in Turkey.
Al-Sakka was apprehended in the southeastern city of Diyarbakir in August as he attempted to board a plane for Istanbul under an assumed name, security sources said.