Investigating judges sent 293 Egyptians to trial on charges of resisting authorities, damaging public property and carrying knives and fire bombs during an anti-government protest last year.
A three-week sit-in in December outside the Cabinet building turned violent when troops badly beat a protester. In four days of clashes that followed, 14 people were killed and hundreds injured.
The defendants, including 24 minors, are also accused of burning a research center housing old manuscripts, attempting to storm the Interior Ministry and practicing medicine without a permit - a reference to the protesters setting up field hospitals to treat hundreds of wounded.
They will be tried in a civilian criminal court.
Egypt's official news agency said on Monday the minors will be tried in a juvenile court. No date has been set for the trial.
This is one in a series of mass trials following violent clashes between protesters and security forces over the past year.
The generals drew international criticism for their crackdown on the December protest, including beating women and pursuing journalists.
Some 379 defendants are also facing trial in July on similar charges that emerged from a November anti-military protest that left more than 40 dead.
One security officer is on trial for attempted murder for allegedly shooting at protesters' eyes.
Another 300 protesters were sent for military prosecution following clashes last week outside the defence ministry. They are likely to face military trials.
The military took over from President Hosni Mubarak, who was ousted in February 2011.
The military's rule has been marred by periodic violence and angry protests by critics of its management of the transition.