The trial reconvened in Baghdad on Monday after a three week recess following the completion of the prosecution case.
Saddam's seven co-accused, including his half-brother Barzan al-Tikriti, were not present as the proceedings began, but arrived in court later.
Saddam and his co-defendants are accused of executing 148 Shia villagers from the town of Dujail, north of Baghdad.
The formal charges read out by Rauf Abd al-Rahman, the chief judge in the trial, included accusations of torture, murder and the execution of minors.
"I charge that you were the president of Iraq... and that you gave orders to security services and the military... to launch an organised attack with various types of weaponry, including helicopters and planes, to kill and then to torture hundreds of Dujailis, including children, and women and men and then to destroy houses and farms," the judge told Saddam, beginning a 15 minute outline of the charges against him.
Asked how he pleaded, Saddam said he could give a simple yes or no answer and insisted he was still Iraq's president.
"I am president of Iraq by the will of the Iraqi people"
"I am president of Iraq by the will of the Iraqi people," he told the judge.
Replying, the judge said: "You were, but not now."
The defence maintains that Saddam and his co-defendants were applying a valid law at the time of the execution, and that the executed were Iraqi citizens plotting with Iran, at war with Iraq at the time, against their own country and leaders' life.
All the accused face hanging if convicted, but only after appeals that will probably be held up by a dozen or so other trials planned against Saddam.
Judge Abd al-Rahman read out
a formal list of charges
According to previous statements by Najib al-Nuaimi, a former Qatari justice minister and member of Saddam's defence team, they plan to call around 30 witnesses in the defence stage of the trial.
The court must approve the witnesses before they give their testimony.
Another member of the defence team, Bushra al-Khalil, said she had had several meetings with Saddam in the past few weeks and that he is ready for the trial.
He is in good health, she said, and had won the respect of his guards. She said he told her that he was not afraid of death, and ready for it.
"He [Saddam] told me does not have high hopes that the final sentence will not be politically motivated," al-Khalil said.
Al-Khalil: Saddam did not know of
Abu Ghraib until he was in court
"He is still isolated from the outer world. He did not know, for example, about the Abu Ghraib scandal until he saw the pictures presented in the court. I and my colleagues always make sure to give him an idea of what is happening around him."
Al-Khalil, a Lebanese Shia, said she was defending Saddam, a Sunni, because she believed that the campaign against him was only because he was an ambitious and patriotic leader.
"His only crime is he tried to build a strong and sophisticated country, and that does not suit the West and some countries in the region.
Al-Khalil said: "Every time I am on board an American helicopter to go to court, or to meet the president, I look at Baghdad and the cement walls that look like snakes wrapping a prey and I am even more confident that they came here and are trying the country's leaders to curb a rising, ambitious Arab-Muslim power."
The trial is expected to recovene on Tuesday with the first witnesses for the defence appearing later in the week.