Iraqi police said clothing found among the remains indicate the victims were a mix of men, women and children, the BBC reported.
The grave in the city south of Baghdad is near a Shiite shrine of Imam Hussein, the Prophet Muhammad's grandson, who died 1,300 years ago.
Police said they believe the bodies are Shiite rebels killed by Saddam Hussein's army after its defeat in the 1991 Gulf War. The Shiite revolt was crushed, and officials estimate as many as 30,000 people were killed.
Saddam and seven members of his regime are being tried in Baghdad for the killing of 148 people in Dujail in 1982, and all have entered pleas of innocent.
Several graves containing thousands of bodies have been uncovered in the Shiite south and Kurdish north since Saddam's fall in April 2003.