Supporters and opponents of the former Egyptian president have clashed outside the police academy in Cairo where the trial is being held.
There had been sporadic trouble since the early hours, and violence broke out again when there was a pause in proceedings. A number of people are reported to have been injured.
Police intervened to try to calm people down. Some 3,000 police officers and soldiers have been deployed to ensure security.
For many people, it was an emotional moment to see the former dictator flown in by helicopter. There had been scepticism that Mubarak would actually appear in the flesh.
Hundreds of people have been gathering outside the complex to watch the trial on a giant screen.
The case has transfixed Egyptians and other Arabs in the wake of this year’s wave of unrest.
Security has also been tightened in Cairo’s Tahrir Square, where protesters again camped out recently calling for a swifter trial for Mubarak and other reforms.