The retrial was ordered after an appeals court in January accepted appeals from the prosecution and the defense.
Mubarak, 85, sat upright on a hospital gurney as he was wheeled into a cage reserved for defendants. Dressed in white prison uniforms, his two sons, Alaa and Gamal, stood alongside him. They face separate charges of corruption.
Mubarak, wearing dark, aviator sunglasses, raised his arm to confirm his presence as the judge read a list of the accused at the start of the session. "Present," said Mubarak, as judge Ahmed al-Rasheedy read the list of names.
The retrial had been due to begin last month but was aborted when the previous judge recused himself.
State TV was broadcasting the court session live.
Mubarak, Adli and four top aides are charged with involvement in the killing of more than 800 protesters who died in the 18-day uprising. His two sons face retrial on charges of financial corruption.
Mubarak`s imprisonment last June was a historic moment - he was the first ruler toppled by the Arab Spring uprisings to stand trial in person.
But the case exposed the difficulties of attaining justice in a country whose judiciary and security forces are still largely controlled by figures appointed during his era.
Many Egyptians have been frustrated by the failure of courts to bring officials to account for the violence during the 18-day uprising and for what they see as decades of corruption and police abuses preceding it.
On Wednesday, an appeals court refused the prosecution`s appeal of a verdict that exonerated two dozen defendants over an incident during the revolt in which men on camels attacked protesters in Cairo`s Tahrir Square.
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