The court said on Tuesday that the new charges of genocide and crimes against humanity had been brought against the ousted Iraqi leader and six co-defendants, paving the way for a new trial.
"We declare the investigations are completed in the case called the Anfal campaign in which thousands of men and women were killed. The accused are being transferred to the criminal court," said Raed al-Juhi, the the court’s spokesman.
Saddam's co-accused will include his cousin Ali Hassan al-Majeed, known as Chemical Ali, and the former defence minister, Sultan Hashim Ahmad, for their roles in a poison gas attack against the Kurdish village of Halabja in 1988 that killed 5,000 people, including women and children.
Human rights groups consider the Halabja attack one of the gravest atrocities allegedly committed by Saddam's government.
"These people were subjected to forced displacement and illegal detentions of thousands of civilians," al-Juhi said.
"They were placed in different detentions centres. The villages were destroyed and burned. Homes and houses of worshippers and buildings of civilians were levelled without reason or a military requirement."
The toppled Iraqi president is already on trial in connection with the killing of 148 Shias after an attempt on his life in the town of Dujail in 1982.
There was no respite from violence for Iraqis on Tuesday. A car bomb exploded in a mostly Shia area of eastern Baghdad, killing at least 10 people.
The bomb went off in Habibiyah and damaged several cars and nearby sandwich stands, police said.
Chaos ensued as fighters from al-Sadr's Mahdi Army militia fired weapons in the air to clear the crowds.
At least a dozen other Iraqis were killed on Tuesday in war-related violence in Baghdad and central Iraq, police said.
Car-bomb attacks continue to
take a heavy toll of Iraqi lives
They included a mother and two of her sons, nine and 12, who died when a bomb exploded in front of their home in the capital.
A third son, age 13, was wounded, along with two brothers from a different family living in the same home, police said.
Elsewhere in Baghdad, a receptionist at the UAE embassy and his friend - both Iraqis - were slain as they left the building, police said.
Armed men also killed a judge, an ice cream vendor and his companion and a policeman in separate slayings in the capital, police said.
In Samarra, 97km north of Baghdad, a car bomb exploded near a convoy carrying the son of a city council member, killing a security guard and a driver, police said. The council member's son escaped injury.
In southern Iraq, armed men killed one policeman and wounded another as the two were driving in the city of Basra, police said.
Two mortar rounds exploded near the British consulate in Basra during a reception, causing no injuries but forcing the party to end early, an Associated Press reporter at the event said.
Police in Baghdad also found the bodies of four men, apparent victims of sectarian reprisal killings. It was unclear when they were slain.
The body of a US marine missing after a weekend vehicle accident was also recovered on Tuesday, the US said.
Six US soldiers were killed and two remain missing after the Sunday accident in western Iraq.