Eight court-appointed lawyers stood in for the defence team, which stayed away in protest at the sacking last week by the Iraqi government of the previous chief judge.
During a noisy exchange while one of the six other defendants quizzed a Kurdish witness, Saddam waved a yellow paper from his seat in the metal pen where the defendants sit.
"I don't want to be in this cage any more," he said.
Presiding judge Mohammed al-Ureybi replied: "I am the presiding judge. I decide on your presence here. Get him out."
The case concerns the Anfal offensive by Iraqi forces in the Kurdish north in 1988.
Saddam and his cousin Ali Hassan al-Majid, known as "Chemical Ali", face genocide charges for what prosecutors say are the deaths of 180,000 Kurds, some of them by gassing. Five others face lesser charges of murder and crimes against humanity.
Villages bombed
Witness Mohammed Rasul Mustafa, a Kurdish man in his 70s wearing a traditional scarf headdress, said he watched aircraft bomb a nearby village, giving off clouds that smelled of apples and gave him breathing difficulties. He was later imprisoned and last saw his wife and five children in jail.
He testified to seeing guards beat a man to death and said 400 to 500 other Kurds died while he was imprisoned.
It’s the second trial that Saddam has faced. A verdict in a year-old trial for crimes against humanity over the killing of 148 Shi'ites is expected next month.