Brotherhood leader Mohammed Badie and his deputy Khairat el-Shater are accused of complicity in the killing of eight demonstrators outside the group's Cairo headquarters on June 30 and early July 1. Badie is currently in hiding, while el-Shater is in custody.
Another senior Brotherhood figure Rashad Bayoumi will face trial on the same charges. Three others face murder charges in the same case.
The clashes came after millions of people had taken to the streets to demand Morsi's resignation. Morsi was deposed by the army on July 3.