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The students have been demonstrating since September, with many of the rallies descending into running battles with police.
Dozens of students were arrested following clashes between police and students at Cairo's famed Al-Azhar University Monday.
The arrests happened during the second day of protests against the military-backed interim government at what is considered the Muslim world's top university for Islamic learning.
The latest round of protests began Sunday after an announcement that 21 students were going to be tried for storming the office of the Grand Imam of Al-Azhar mosque several weeks ago.
Police fired tear gas, and students set fire to a police vehicle. The government accused the students of throwing molotov cocktails at police.
Last month, 12 students from Al Azhar were sentenced to 17 years and given large fines for clashes on campus.
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Also on Monday, the leader of Egypt's Muslim Brotherhood, Mohammed Badie, appeared in court for the first time.
Badie appeared with 14 other Brotherhood leaders who face charges of inciting violence.
The leaders of the Muslim Brotherhood were swept up in a crackdown against the Islamist group since the July 3 coup that removed President Mohamed Morsi from power.
Morsi is on trial for conspiracy to murder, among other charges.
According to the Associated Press, the defendants on Monday chanted, "Down with military rule," from the prisoner's box.