The hearing opens a new legal chapter for the former Iraqi leader who once again faces a possible death penalty for the systematic killing of tens of thousands of Kurds during the Iraqi army's operation Anfal during the eighties.
Saddam initially refused to identity himself to the court and after being pressed by to do so he lashed out at Judge Abdallah al-Ameri, accusing him of working on behalf of the US forces which invaded Iraq in March 2003.
"You are here in the name of the occupier not in the name of Iraq. My name is known to Iraqis and to the world," Saddam declared.
He introduced himself as "Saddam Hussein, the President of the Republic of Iraq and the commander-in-chief of the Iraqi armed forces."
But when the time came to enter a plea, Saddam refused, and the judge ordered that a plea of "innocent" be entered into the record.
It is believed that at least 100,000 Kurds were killed during 1987 and 88 and more than 3,000 villages destroyed.
Prosecutors describe the campaign as an act of genocide against the Kurdish people, while the former Iraqi government defended its actions as a necessary counter-insurgency operation during wartime.
The crackdown was allegedly aimed at crushing independence-minded Kurdish militias from the northern region along the border with Iran. Saddam accused the Kurds of helping Iran in its war with Iraq.
Kurdish survivors say many villages were razed and countless young men disappeared.
They also accuse the army of using prohibited mustard gas and nerve agents, but the trial does not deal with the most notorious gassing - the March 1988 attack on Halabja that killed an estimated 5,000 Kurds. That incident will be part of a separate investigation by the Iraqi High Tribunal.
The proceedings are taking place in the same courtroom where Saddam spent months jousting with the judges in his turbulent first trial.
That case was over the killings of more than 148 Shi'ite Muslims from the town of Dujail in a crackdown launched after a 1982 assassination attempt on Saddam.
Verdicts for Saddam and seven co-defendants are expected in that case on October 16.
The Dujail trial was plagued by frequent outbursts by Saddam and his co-defendants, who repeatedly challenged the legitimacy of the tribunal, saying it was created by the Americans, whose forces swept Saddam's regime out of power in the 2003 invasion of Iraq.
Saddam appeared ready to show the same defiance in his new trial - as did his top co-defendant, Ali Hassan al-Majid, who allegedly led Operation Anfal became known as "Chemical Ali" for the use of poison gas.
Al-Majid walked into the court, using a cane and wearing a red headscarf, and proudly identified himself as "Fighting comrade First Major General Pilot Ali Hassan al-Majid."
The prosecution then began its opening statement, saying "the order (to launch the Anfal campaign) was issued by the defendant Saddam Hussein."
"The goal was clear - to target the people of Kurdistan through killings, forced migration, persecution and denying them their personal freedoms," the prosecutor said.