Brotherhood Supreme Guide Mohammed Badie and other leaders of the Islamist grouping including Essam al-Erian and Mohammed al-Beltagui face charges of inciting violence in the Cairo neighbourhood of Bahr al-Aazam that led to deadly clashes in July.
Badie and his two deputies Khairat al-Shater and Rashad Bayoumi in a separate trial already face other charges related to the deaths of protesters who stormed the Brotherhood's Cairo headquarters on June 30.
In October, the original judges presiding over that case recused themselves, citing "reasons of conscience".
The trials are part of a massive crackdown by authorities against the Brotherhood after the military overthrew Islamist president Mohamed Morsi in July.
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Security forces launched a sweeping crackdown on Morsi's supporters in August, violently dispersing two protest camps in the capital.
More than 1,000 people have been killed since Morsi's ouster -- mainly his supporters -- and the authorities have arrested some 2,000 Islamists, including most of the Brotherhood's leadership.
Morsi himself is on trial over his alleged involvement in the deaths of protesters outside the presidential palace in December 2012.
The army ousted Morsi, Egypt's first democratically elected president, on July 3 after millions of people took to the streets to demand his resignation, accusing him of betraying the revolution that brought him to power.