Dressed in white prison outfits, Alaa and Gamal -- once the symbols of wealth and power -- faced accusations of insider trading along with seven other defendants.
The pair had faced different corruption charges along with their father in a separate trial, but the court dropped them due to the expiry of a statute of limitations.
They have remained in prison pending investigations into the new case.
On June 2, a court sentenced Hosni Mubarak and his interior minister to life in jail for their involvement in the killing of protesters during the uprising that ousted the former strongman in February 2011.
Gamal, 48, headed a powerful policy committee in the ruling party under his father and was widely seen as the heir apparent, a perception that helped fuel the uprising against Mubarak.
Alaa, the older son, stayed out of politics but was rumored to have amassed a fortune using his father's connections.