After a two week break, proceedings rapidly became embroiled in the wrangling that has marked previous sessions as the chief judge rejected calls by the defence team for the trial to be postponed and for the judge and chief prosecutor to be dismissed.
Saddam and seven former aides, who were all present, are charged with crimes against humanity.
The resumption of the trial on Tuesday came against a background of deadly unrest in Iraq, which included the bombing of the tomb of Saddam's father in his hometown, Tikrit.
In court on Tuesday, Saddam's lawyers repeated their demand that chief judge Rauf Abd al-Rahman be sacked, saying he is biased and prejudiced.
Ramsey Clark, the former US attorney-general who is helping to defend Saddam, has submitted a motion recently claiming the judge "is not impartial and has a manifested bias against the defendant".
He has "repeatedly violated standards of fair trial, human rights and basic due process in the courtroom", Clark said.
The defence says Abd al-Rahman is biased because he is a native of the Kurdish village of Halabja, the target of a 1988 chemical attack in which about 5000 people, including women and children, died.
Saddam's lead lawyers then walked out of the courtroom and were replaced by court-appointed lawyers.
The opening of the trial had earlier been delayed by several hours, the reasons for which were unclear.
After a stormy 12th hearing on 14 February, when a defiant Saddam announced he was on hunger strike amid chaotic scenes, Abd al-Rahman adjourned the trial to 28 February.
"[The chief judge] has repeatedly violated standards of fair trial, human rights and basic due process in the courtroom"
former US attorney-general
But Saddam's lead lawyer, Khalil al-Dulaimi, said on Monday that the deposed president had ended his fast to protest against court proceedings, and indicated that the defence team could be ready to start attending the trial again.
The bombing of Saddam's father's tomb occurred at 7am (0300 GMT) in the al-Arbain graveyard, in the centre of the northern town of Tikrit where Hussein al-Majid's tomb was built by Saddam.
The second phase
The trial has frequently run into trouble, with stormy sessions featuring long outbursts or walkouts by the defendants and their counsel as well as the resignation of the previous chief judge and the killing of two defence lawyers.
The trial is currently in the second phase of depositions by witnesses testifying over events during the Dujail massacre.
Since Abd al-Rahman took over as chief judge, Saddam has often been locked in heated verbal exchanges with him, often plunging the sessions into chaos.
Saddam and the other defendants face the death penalty if found guilty of the killing of more than 140 people from Dujail in 1982 allegedly in retaliation for an assassination attempt against him.