The three judges presiding in the trial of Muslim Brotherhood chief Mohamed Badie and his aides withdrew from the proceedings at the start of a session on Tuesday.
Prior to their decision to step down the judges ordered that the defendants continue to be held in custody, an AFP correspondent in the court said.
Badie and his two deputies, Khairat al-Shater and Rashad al-Bayoumi, face charges related to the deaths of protesters who stormed the Brotherhood's Cairo headquarters on June 30.
A total of 32 other defendants are being prosecuted along with Badie, Shater and Bayoumi. None of the 35 defendants were in the court on Tuesday.