The two — Mohammad Cholily and Abdul Azis — are the first of four men accused in the triple suicide bombings, which killed 20 people and were blamed on the Al Qaeda linked Jemaah Islamiyah terror group.
All are accused of supplying and transporting explosives to be used in blasts, and sheltering Noordin Top, an alleged Jemaah Islamiyah leader believed to be the ringleader of the Oct. 1, 2005 bombings.
Hundreds of police guarded the courthouse in Denpasar, Bali's main town and a short journey from the scene of the bombings in two of the island's main tourist districts.
Prosecutors were scheduled to read out their indictments against the men, who will not be required to enter a plea or respond to the charges in Tuesday's hearings.
The men are being tried individually, in separate courtrooms, under anti-terror legislation that carries the death penalty.
Jemaah Islamiyah has been blamed for a series of attacks in Indonesia in recent years, including attacks on Bali in 2002 that killed 202 people, most of them foreign tourists.
Courts on Bali sentenced three militants to death for planning and carrying out those blasts.
The three, who are among more than 200 suspected Islamic terrorists arrested in Indonesia in recent years, are on death row.