On Sunday, Rizgar Amin said from his home in the Kurdish city of al-Sulaimaniya, 260km northeast of Baghdad, that he wanted an Iraqi Shia to take control of the proceedings.
"I am happy that I am no longer part of this trail. I am happy to watch it on television while sitting in my house," Amin said.
Amin was replaced by fellow Kurd Rauf Abd al-Rahman as chief judge.
He cited health reasons for his decision, but politicians, mostly Shias, had complained about the slow pace of the proceedings and Amin's patience in the face of frequent outbursts by Saddam and one of his co-defendants, Barzan Ibrahim al-Tikriti.
The new judge's appointment was a surprise to many as Amin's deputy, Said al-Hammash, had been expected to take over but was moved off the case after allegations he was once a member of Saddam's Baath party.
Al-Hammash, a Shia, denied Baath membership and maintained he was the victim of a conspiracy.
Amin made no direct reference to either Abd al-Rahman or al-Hammash, but said he wished a Shia would take charge of the trial so he could see how they would control the often chaotic proceedings.
"I wish that the trial was run by a Shiite judge because I want to know how they are going to manage it," he said.