Family members stood outside the courthouse screaming after the verdict - the biggest mass death sentence handed out in Egypt's modern history, defence lawyers said.
Turmoil has deepened since the army overthrew Egypt's first freely elected president, Mohamed Mursi of the Muslim Brotherhood, in July. Security forces have killed hundreds of Brotherhood members in the streets and arrested thousands.
Human rights groups said the verdict suggested the authorities intended to tighten their squeeze on the opposition.
Most of the defendants at yesterday's hearing were detained and charged with carrying out attacks during clashes which erupted in the southern province of Minya after the forced dispersal of two Muslim Brotherhood protest camps in Cairo on August 14.
Islamist militants have also stepped up assaults on the police and army since Mr Mursi's removal, killing hundreds and carrying out operations against senior interior ministry officials.
Defence lawyer Ahmed al Sharif said: "The court has decided to sentence to death 529 defendants, and 16 were acquitted." The condemned men can appeal.
The Muslim Brotherhood, largely driven underground, responded by calling for the "downfall of military rule" on its official website.
Mohamed Mahsoub, who served as minister of legal affairs under Mr Mursi, described the court's decision "a ruling calling for the execution of justice".
The charges against the group, on trial in Minya since Saturday, include violence, inciting murder, storming a police station, attacking persons and damaging public and private property.
Mohamed Zaree, of the Cairo Institute for Human Rights Studies, said: "A second year student in the faculty of law would never issue this verdict. There are a lot of flaws in this verdict."