Saddam sat fuming in the Iraqi High Tribunal along with six co-defendants, accused of leading the savage eight-month Anfal campaign in 1988 against Iraq's Kurdish minority.
The furious 69-year-old claimed to be "President of the Republic of Iraq", clashed angrily with the prosecutor over rape claims and shouted at the judge after two of his lawyers were banned from speaking.
Saddam's cousin Ali Hassan al-Majid - nicknamed "Chemical Ali" because of his alleged fondness for using poison gas - also refused to plead, but the judge ordered that "innocent" pleas be recorded for both men.
The start of the case was marked in the Kurdish region of northern Iraq by five minutes of silence on behalf of Anfal's victims.
"I urge you to listen carefully to the details of these events... It is difficult to fathom the barbarity of such acts," lead prosecutor Munqith al-Faroon said.
Photos of mass graves
Prosecutors showed the court photographs of mass graves - including one in which the body of an infant child still sucking a milk bottle was buried next to his mother - and detailed the eight stages of the Anfal campaign.
Beginning on February 22, 1988, the Iraqi air force allegedly began firing chemical weapons into the Juwaid Valley outside the northern city of Sulaimaniyah. This was followed up with an artillery barrage, the court heard.
The prosecutor charged that over the next eight months troops were sent into Kurdish regions, repeatedly using poison gas, as whole villages were isolated and attacked, the prosecutor charged.
"Women, children were transferred to detention centres made in advance. Detainees suffered harshly. Camps had no basic services. Detainees were exposed to torture, insults and non-potable water," the lead prosecutor said.
"Those who died were buried outside the camps by the detainees and later animals were set free to dig up those graves, mostly in the Samawa desert.
"Women were put through psychological torture. Their infant babies were separated from them. The babies and the mothers were allowed to cry. Young women were raped by guards and officials," he told the court.
Angry response
In response to prosecutor Faroon's rape allegation, Saddam angrily replied: “If he says that a Iraqi woman was raped in my era and if he does not prove it, I will hunt him for the rest of my life”.
"An Iraqi woman raped in my era? The reign of Saddam Hussein? Saddam will not accept it. If I hear that during my reign this happened, and if he does not prove it, he will be my enemy. Saddam will not accept it.”
The chief judge later called a halt to proceedings and said the case would continue today after dismissing a claim from Saddam's defence counsel that the Iraqi High Tribunal has no legitimacy to try the case.
The defence is expected to argue that Anfal was a legitimate counter-insurgency operation against Kurdish separatist guerrillas who sympathised with the Iranian side in the Iran-Iraq war from 1980-1988.