On January 15, 2006, the Iraqi High Court issued a statement confirming that presiding judge Amin resigned due to "personal reasons." On January 23, a spokesman for the special court that tried Saddam said that the court decided to appoint Rauf Abdul Rahman as the presiding judge. On January 29, shortly after the retrial of Saddam's case, Saddam's defense team, Saddam himself, and several other defendants left the court to protest against the procedural issues of the special court. On February 1, the Iraqi High Court's trial against Saddam began again, but Saddam himself and his team of defense lawyers did not attend the trial. On February 13, Saddam appeared in court for another trial and chanted the slogan "Down with Bush." On February 14, Saddam declared in court that he and the other three defendants had started a "hunger strike" to protest the "unfair trial" carried out by the presiding judge and his superiors. On February 27, Saddam's chief defense lawyer al-Duraimi revealed that Saddam had stopped his 11-day hunger strike a week ago due to health reasons.

Saddam admitted in court that after the incident in Dujar Village, he personally ordered retaliation against the villagers. Saddam, who testified directly in court for the first time, called his trial a "farce." When Saddam appeared in court for trial, he lashed out at the Iraqi Interior Ministry for killing thousands of Iraqis and demanded that international agencies authenticate his signature on relevant documents produced by prosecutors. Saddam and seven co-defendants appeared in court again for trial. The judge read out a criminal expert's report saying that Saddam's signature on the original document related to the death penalty for the villagers of Dujar Village was authentic. Saddam's defense lawyer said that these identification experts are members of the Ministry of Interior and "because of their relationship with the Ministry of Interior, they cannot be independent." He asked the court to appoint other experts to re-authenticate the signatures. Saddam's defense lawyer accused the prosecution witness Haidri of perjury during the trial and asked the court to investigate the reliability of the testimony of all prosecution witnesses.

Hamis al-Obeidi, one of Saddam's main defense lawyers, was kidnapped by militants and killed. Saddam and seven other defendants began a hunger strike to protest the shooting of al-Obeidi. The US military in Iraq said Saddam has ended his hunger strike. Saddam and his lawyers once again refused to attend the trial in protest of al-Obeidi's killing. Saddam was sent to the hospital for treatment after going on hunger strike for many days. Saddam appeared at the trial and said he was forcibly brought to the court. He also said that if he was sentenced to death, he would like to be shot rather than hanged. The Iraqi High Court announced the verdict in the Dujail village case, and Saddam was sentenced to death by hanging for murder and crimes against humanity.