The trail resumed on Monday despite a boycott by Saddam's defence lawyers.
The former presidnet and six of his officials are accused of ordering the 1988 Anfal campaign by Iraqi forces in which 182,000 Kurds were killed, prosecutors say.
The court heard testimony from a Kurdish woman who accused Saddam Hussein of burying her family in a mass grave.
She spoke from behind a curtain to protect her identity.
She said Iraqi forces attacked her village in April 1988 when she was 13-years old and rounded up members of her family.
"I know what happened to my family. They were buried alive," she told the court.
The prosecutor said that her relatives' identity cards had been found at a mass grave near Hadhar in northern Iraq.
When the survivors came down from the hills, they were rounded up and she, her mother and their neighbours were taken to Saddam's hometown of Tikrit, where the men were separated from the women, she said.
Once at Nigrat Salman prison, the women were held in humiliating conditions.
"When we were allowed to go to the bath, we used to do it in front of the soldiers because the place was surrounded by razor-wire," she said, adding that soldiers fired over her head.
Saddam sat in the dock in his trademark dark double-breasted suit, looking uninterested, ignoring proceedings and reading a book.
But Saddam's lawyers had said on Sunday that they would maintain their boycott, in protest at what they said was Iraqi government interference in the case, particularly the sacking of a former chief judge.
His fellow defendants face a lesser combination of charges, but all seven could face the death penalty if convicted by the Iraqi High Tribunal.
Legal rights groups have meanwhile said that the dismissal of Abdullah al-Amiri - removed by the government for saying the toppled Iraqi leader was "not a dictator" - could hurt the trial's credibility.
Court-appointed lawyers are now defending the former Iraqi leader and his six co-defendants.
Saddam, 69, his cousin, Ali Hassan al-Majeed, and five former commanders face charges of war crimes and crimes against humanity for their role in the 1988 Anfal campaign that prosecutors say left 182,000 ethnic Kurds dead or missing.
Saddam and al-Majeed also face a charge of genocide. All face the death penalty.
Saddam is waiting for a verdict from a first trial for crimes against humanity in the killing of 148 Shia men from the town of Dujail in the 1980s.
The Anfal trial has featured testimony from villagers recounting their suffering, when Saddam's forces are alleged to have attacked Kurds, razing villages and killing and displacing thousands of people.
Defendants have argued the attacks were legitimate military strikes against Iraqi Kurds fighting alongside Shia Iran against Saddam's Sunni-led government during the Iraq-Iran war.
The court trying Saddam for the Dujail deaths - whose first chief judge quit, citing political interference - is due to reconvene on October 16 to review witness testimonies.