“Some were shot in their sleep, some cut up with machetes to preserve bullets. Others were burned alive after their houses were set on fire,” Luis Moreno Ocampo said in his opening statement.
The two alleged commanders, Germain Katanga, 31, and Mathieu Ngudjolo, 39, both pleaded not guilty to three crimes against humanity and seven war crimes, including murder, rape, sexual enslavement and pillage.
Defence attorneys for the men denied their involvement.
They called on judges to investigate the role of Ugandan and Congolese authorities in the massacre.
It was only the tribunal’s second trial since it began operations in 2002.
The first case, of alleged Congolese warlord Thomas Lubanga who is accused of recruiting child soldiers, started in January.
Prosecutors say Katanga and Ngudjolo led two mobs of child soldiers and older fighters armed with automatic weapons, machetes and spears to destroy the village of Bogoro in Congo’s mineral-rich Ituri province on February 24, 2003. Many of the victims were hacked to death.
The village was strategically located on a crossroad and was the base of a rival militia known as the UPC, which was led by Lubanga.
Moreno Ocampo said the attack went far beyond a legitimate military campaign to become revenge for earlier UPC attacks.
“The plan was to wipe out Bogoro,” he said.
“Destroy not only the UPC camp but the whole village.”
But Ngudjolo’s defence attorney, Jean-Pierre Kilenda, blamed the attack on Ugandan forces who were occupying Ituri and wanted to root out the UPC after an alliance between the two groups soured.
“It could be said that the plan to throw the UPC out of Bogoro was hammered out by the highest authorities in Uganda and Congo,” he said.
Katanga and Ngudjolo both sat impassively as Moreno Ocampo outlined his case, accusing their soldiers also of raping women and forcing others into marriage or sexual slavery.
Moreno Ocampo quoted Katanga as boasting after the attack that “nothing was spared”.
“Absolutely nothing. Chickens, goats, everything ... was wiped out.”
Lawyers for some 345 victims — including some of the child soldiers forced to carry out the massacre — also are taking part in the trial.
“Their childhood was brutally interrupted and they have been in hell from one day to the next,” said Belgian attorney Jean-Louis Gilissen, who is representing child soldiers.
He said that the children were abducted and ordered to fight “as vanguard troops for the butchery of Bogoro”.
Another victims’ lawyer, Fidel Nsita Luvengika, said establishing the truth will allow his clients to mourn slain family members.
“They don’t know what happened to their families. They don’t know how they were killed or whether they were buried,” he said.
Prosecutors plan to call 26 witnesses to support their case. In an indication of the ongoing climate of fear in Ituri, 21 of them will testify with their identities shielded from the public.
Among other cases at the world’s first permanent war crimes court, former Congolese vice president Jean-Pierre Bemba is in custody and scheduled to go on trial next year for alleged crimes in the Central African Republic. Sudan’s President Omar al-Bashir and two other Sudanese have been charged with atrocities in Darfur. The leaders of brutal Ugandan rebel group the Lord’s Resistance Army also are under indictment.