Organised by the Muslim Brotherhood, Egypt's most potent opposition force, protests were staged at four universities in Cairo and several other cities under the slogan "Together for reform: Free university ... Free country".
"State security is everywhere on campus," said 24-year-old demonstrator Alaa Alam.
"We have no freedom to do anything. The security services do not only target us religious Muslims, but everyone in our country's universities.
"There is a movement for reform in Egypt, and we are part of it. We are not asking for something extraordinary, we are just demanding our rights."
Alam was speaking outside Cairo University where 600 students - some of them wearing mock handcuffs and masking tape on their mouths - demonstrated.
They were surrounded by hundreds of riot police.
The students demanded the immediate release of all political detainees and urged the government to organise free elections starting on 8 November.
Female students hold signs next
to police at Cairo University
The Muslim Brotherhood is officially illegal and could not field a candidate for the 7 September presidential election but is nevertheless expected to make a strong showing in the parliamentary polls, where its candidates run as independents.
It was the first time the banned but tolerated movement organised a university protest under its name, rather than under the looser Islamist banner.