With Egypt now under an army-installed government after last month's overthrow of Islamist President Mohamed Mursi, local media seized on the symbolism of both hearings happening on the same day. "Trial of two regimes" was the headline in the al Shorouk daily.
Mohamed Badie, the Brotherhood's "General Guide", and two deputies did not appear at the opening of their trial for security reasons, and the judge adjourned proceedings until October 29.
The case against them relates to unrest before the army removed Mursi, who has been detained ever since.
Since Mursi's fall more than 1000 people including about 100 soldiers and police have died in violence across Egypt, the bloodiest civil unrest in the republic's 60-year history.
Former president Mubarak was sentenced to life in prison last year for complicity in the killing of protesters during the 2011 revolt against him, but an appeals court ordered a retrial. He was bailed on Thursday after judges ordered his release.
He appeared in a courtroom cage in a wheelchair, dressed in white, with his jailed sons Gamal and Alaa and former interior minister Habib al-Adly.
After a three-hour hearing the case was adjourned until September 14.