Clashes between security forces and supporters of the outlawed Muslim Brotherhood on Wednesday left two dead and 30 injured across five governorates, according to the health ministry.
The renewed protests were part of a campaign by the pro-Brotherhood coalition the National Alliance to Support Legitimacy (NASL), which earlier this week called for protests beginning on Wednesday and continuing for the next 11 days to mark the three-year anniversary of a constitutional referendum the Brotherhood supported on 19 March 2011.
Universities in the cities of Mansoura, Beni Suef and Cairo – including Cairo University and Al-Azhar University – witnessed clashes between pro-Brotherhood students and security forces.
In Beni Suef, Amr Mohamed Ali Kafaty, 13, was shot dead outside of Beni Suef University's campus when clashes erupted between police and students, according to the health ministry.
Meanwhile, state-run news agency MENA reported that two female engineering students from Cairo University had been injured by live ammunition in Wednesday's clashes on the campus.
According to eye witnesses, security forces had not been present when the two students were shot.
Witnesses also reported birdshot being fired from the roof of the university's buildings.
Five other students were injured in the day's protests, three at Beni Suef University and two at Al-Azhar University, the health ministry said.
The NASL claims of two students killed in Beni Suef and another at Alexandria University have not been confirmed.
Police fired teargas to disperse dozens of students marching from Cairo University to the Giza security directorate, Al-Ahram's Arabic news website reported.
Police also entered Al-Azhar University's campus to disperse student protesters.
Dozens of students were arrested during protests at universities across Egypt.
Students formed human chains at a number of universities, but were quickly dispersed by the police.
Other rallies were also held by Brotherhood supporters in several governorates including Sharqiya, Gharbiya, Damietta and Beheira.