Ali Muhammad Ali Abd-al-Rahman is accused of overseeing pro-government Janjaweed fighters responsible for the persecution, murder, rape and torture during the peak of the 2003–2004 violence in which hundreds of thousands of people were killed.
Seventy-year-old Abd-al-Rahman told the judges, “I am acquitted of all these charges,” after the charges were read out at the beginning of his case.
Abd-al-Rahman, who prosecutors say was also known as Ali Kushayb, voluntarily surrendered to a court in The Hague in June 2020 after 13 years on the run. He has denied the allegations.
The test comes amid a surge in what humanitarian groups say since the end of the UN and African Union missions.
Even decades after the worst fighting, 1.6 million people are still internally displaced in Darfur, the United Nations estimates.
The conflict in Darfur first erupted when most non-Arab rebels took up arms against the government of Sudan, which responded by revolt.
Khartoum launched a wave of violence that Washington and some activists called genocide, mostly Arab militias, known as Janzweed, to quell the rebellion.
The United Nations estimates that 300,000 people were killed and more than two million were evicted from their homes.
Abd-al-Rahman has been charged with 31 counts of war crimes and crimes against humanity and could face life imprisonment if convicted.
During the earlier hearing, his counsel argued that the defendant was a victim of mistaken identity and was not educated enough to understand the orders passed by him which could be a war crime.
Former Sudanese President Omar Hassan al-Bashir, who is facing ICC charges for the genocide and other atrocities in Darfur, was deposed in 2019 and remains in jail in Khartoum.