A Kurdish villager, meanwhile, testified that women prisoners were often raped during the brutal 1987-88 Anfal attacks against the Kurds that prosecutors say left 182,000 people dead.
Saddam was thrown out when he waved a sheet of yellow legal paper from the dock, declaring: "I have a request here that I don't want to be in this cage any more."
But Judge Mohammed Al Oreibi Al Khalifah fired back: "I am the presiding judge. I decide about your presence here. Get him out."
Bailiffs took Saddam out of the courtroom and the hearing at the Iraqi High Tribunal in Baghdad - where Saddam is facing charges of genocide, war crimes, and crimes against humanity - continued.
Saddam and six of his former colleagues face charges for spearheading the Anfal military campaign.
They face the death penalty if found guilty.
Khalifah took over as the trial's new chief judge last week after his predecessor Abdullah Al Ameri was accused of showing leniency and sacked by the Iraqi government.
"You need to show respect to the court and the case, and to those who don't show it, I am sorry, but I have to apply the law," Khalifah told another defendant, Sabir Al Duri, who was questioning the day's first witness.
Saddam's defense team was not in court. The former Iraqi president's counsel boycotted the trial Monday, accusing the government of interfering with the court proceedings.
Last week, the Iraqi government sacked Ameri after he told Saddam in open court that he had not been a dictator. He was quickly replaced by his deputy, Khalifah.
"The defense team will not recognize the legitimacy of this court and does not accept the tailor-made decision taken by the occupying forces," chief defense attorney Khalil Al Dulaimi had said in Amman Sunday. "It is not about this judge or that judge, but from day one we have protested the legitimacy and the bias of this court," he argued.
On Monday Duri, the director of military intelligence under Saddam, referred to another accused and former defense minister Sultan Hashim Al Tai by his rank, irritating the judge.
Saddam responded by demanding to be excused, whereupon Khalifah ejected him, as he had done September 20 when the defendant had protested against the replacement of the former trial judge.
Khalifah has provided eight court-appointed lawyers for the defendants.
Last week, government spokesman Ali Al Dabbagh said that the decision to transfer Ameri was taken to preserve the "neutrality of the court."
The latest events have provoked strong criticisms from international legal experts, who fear for the impartiality of the hearings.
Nehal Bhuta of the New York-based Human Rights Watch, a long observer of the trials, said that the judge's removal was "a blatant violation of the independence of the court."
A senior Iraqi government official said that the government intervened "as this was the trial of Saddam Hussein ... the man who has killed thousands. Anyone who says he was not a dictator will not be tolerated by the people."
Kurdish witness Rifat Mohammed Said, meanwhile, testified Monday how his village was gassed and bombed and told of atrocities in the southern Nugrat Salman prison where he was held along with hundreds of others.
He said that women detainees often complained of rape by Hajaj, the man who ran the prison.
Said said that every day one of the imprisoned women would be taken to the room of Hajaj.
"The girls came back crying and told us they had been subjected to rape," Said said from the witness-box.
While men and women in the prison were kept in separate cells, they were able to communicate with each other.
He also said that "some days, two or three children were dying" in the prison due to hunger.
Two other witnesses also testified Monday before the court was adjourned to Tuesday.
Mohammed Rasul Mustafa, a Kurdish villager, told the court how he witnessed the guards "kill a man with a steel cable" in the Nugrat Salman prison.
He said that at least 400 prisoners died, mostly old people.
When he was released, he returned home to find his whole family - his wife and five children - missing.
The day's third witness Fahima Amin Karim, broke down during her testimony, in which she recounted her daughter's death from chemical attacks.
"I was holding her when she died, they took her away, I don't know where. I don't even know where she is buried," she said as she wiped her tears.
Many of her relatives were also killed during the attacks, she added.
© 2006 Agence France-Presse
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