Ahmed Hassan Mohammed testified against Saddam and seven co-defendants in the mass arrests and killings of 148 Shiite men in the village of Dujail, following an attempt of the former leader's life.
Up to 10 witnesses are scheduled to testify, some of them with their identities concealed, which analysts told the BBC will make it difficult for the defense to rebut their testimonies.
The trial was delayed by about 90 minutes when civil rights advocate and former U.S. Attorney General Ramsey Clark and Saddam's defense team walked out of the Baghdad courtroom. Clark wanted to present oral arguments contending that the trial is unfair because of the threats of violence surrounding the proceedings, and because the special tribunal was originally conceived by U.S. authorities.
Also before Monday's session, one of the five judges recused himself, citing a potential conflict of interest, as one of the co-defendants may have been involved in killing his brother.