Initially, the ousted Iraqi leader refused to identity himself, but after being pressed to do so 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 told the judge.
Saddam is being tried along with six former army commanders all charged with killing tens of thousands of Kurdish villagers in a campaign known as Operation Anfal in the late 1980s.
As proceedings began he introduced himself as "Saddam Hussein, the president of the Republic of Iraq and the commander-in-chief of the Mujahidin (the Iraqi armed forces)".
The judge ordered a plea of "innocent" to be entered into the record after Saddam refused to answer.
Saddam was later angered by prosecutors who claimed that Kurdish Iraqi women were raped in prison during his presidency.
"I can never accept the claim that an Iraqi woman was raped while Saddam is president," he shouted, banging on the podium in front of him and pointing a finger at the prosecutors. "How could I walk with my head up?"
One of Saddam's co-defendants is his cousin, Ali Hassan al-Majid, known as "Chemical Ali" because of poisonous gas attacks he is alleged to have been behind. He also refused to enter a plea.
The defence team of the former president, already awaiting a verdict in another trial on charges of killing 148 Shia Muslim men and boys, challenged the legitimacy of the special tribunal.
"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"
Ousted Iraq president
The tribunal "was established by an occupation entity," Khalil al-Dulaimi,Saddam's chief lawyer, said in his opening statement, "and occupation authorities have no right to establish courts".
The seven defendants face charges for their role in military offensives codenamed Anfal (Spoils of War) after the title of a chapter of the Quran.
Iraqi forces are accused of launching mustard gas and nerve agent attacks in the Anfal campaign, seen as one of the most potent symbols of Kurdish suffering under Saddam.
"It's time for humanity to know ... the magnitude and scale of the crimes committed against the people of Kurdistan," Munqith al-Faroon, the lead prosecutor for the Anfal case, said in his opening statement.
All seven accused face charges of war crimes and crimes against humanity for the seven-month onslaught. Saddam and al-Majid also face the more serious charge of genocide, which carries the death penalty.
Many villages were razed and hundreds of thousands of people were displaced or killed during the attacks.
Saddam and his co-accused are likely to argue that their crackdown was justified because Kurdish rebels and their leaders had committed treason by forming alliances with Iran.
About 60 to 120 witnesses are expected to appear before the court. The judges also will review more than 9,000 documents.
After a the opening session, which lasted nearly five hours, the trial was adjourned until Tuesday.