The new charges are based on the deaths of thousands of Iraqi Kurds against the former Iraqi president and six of his former deputies including "Chemical Ali" Hassan al-Majid.
The new charges, which pave the way for a second trial, implicate Saddam in the Anfal campaign in northern Iraq in the 1980s.
Operation Anfal included the March 16, 1988 gas attack on the village of Halabj where an estimated 5,000 people, including women and children, died, and is regarded as one of most egregious human rights abuses in Saddam's 24-year regime.
"It was during this campaign that thousands of innocent women, children and men were buried in mass graves," said chief judge Raid Juhi at a news conference. "The natives of Kurdistan suffered very hard conditions."
Saddam and seven others are currently on trial for the torture and killing of 148 Shiite men and boys in the Iraqi village of Dujail in 1982, though none of Saddam's codefendants in the Dujail case are implicated in the Anfal genocide charges.
The Iraqi court decided to hear the charges for the 1982 massacre first because the evidence in the case that ties Saddam and his codefendants to the execution order is much clearer than for other alleged crimes.
The Dujail case begins its last phase Wednesday, when the court will hear final arguments from the defense and prosecution, but officials predict that the trial run at least until May.
It is not clear whether the Iraqi High Tribunal's investigative court will hear the new charges at the same time as the Dujail charges, or wait until a verdict is rendered.
If Saddam is found guilty and sentenced to death, he may escape being tried for the charges tied to the deaths of thousands of Kurds, which still resonates among the Kurdish community -- many members of which see the trial of Saddam as a distraction and call for his immediate execution.
If the new charges are brought concurrently, the defense will face the burden of fighting two cases at the same time, while a second prosecution and panel of judges begins preparing witnesses and evidence for the Anfal genocide.
This new trial may also give Saddam another turn at the witness stand, an opportunity he last used to denounce the High Tribunal, call for Iraqi resistance against the Americans, and advance his claim that he is still president of Iraq.
Judge Raid Juhi has said it is too early to speculate about the details of the new case, which is expected to begin in the next 45 days.
The new charges come after one of the bloodiest days of the year in Iraq that saw the deaths of 24 Iraqi civilians in three car bombings across the country, and nine U.S. soldiers in the insurgent stronghold Anbar Province, the highest single-day total for American forces since Jan. 5.
U.S. military officials also reported this month that 1,313 Iraqi civilians were killed from Feb. 22 to March 22.