The rebellion was encouraged by the United States but crushed without American intervention by Saddam Hussein.
Fragments of watches, a woman's blue slipper, bloody clothing and pieces of traditional black cloaks often worn by Iraqi women were found at the gravesite, some 13 miles northwest of Najaf, one of the most holy cities for Shiite Muslims. Bullet casings also were found near the graves.
More than 25 bodies were unearthed Saturday, and at least 10 had been identified, local Iraqis said. About 47 sets of remains, including those of women, were uncovered Sunday afternoon. The men and women were apparently lined up and shot.
Some bodies had identification cards in their pockets.
"I'm looking for my own relatives," said Jawad Shaker, who came to the site on Sunday. Another person said he was looking for his nephew who disappeared in 1991.
In other developments:
The Supreme Council for the Islamic Revolution in Iraq, a Shiite group, was directing the excavation of the mass grave site and said it was preparing a special section of a cemetery to rebury those who it called the "martyrs"' of 1991.
Tens of thousands of people were killed after Iraq's Shiite majority rose up with the encouragement of the United States after the 1991 Gulf War and seized control of most of the southern part of the country. Shiites, a minority in the Islamic world, make up 60 percent of Iraq's Muslims and were ruled for a generation by Saddam Hussein's overwhelmingly Sunni Muslim Baath Party.
Iraqi forces used helicopter gunships and tanks to defeat the lightly armed rebels. The United States controlled Iraq's skies at the time but did not intervene. Thousands of people are believed to have been executed after the failed revolt.
On Sunday, five people were digging at the site. Farmers in the area said they had known about the site for years but were scared to talk about it while Saddam was still in power.
One farmer, who refused to give his name, said he saw people blindfolded and shot in the back of the head after the uprising.
"Everybody knew and could see, but they kept quiet," said Kamel al-Tamini, another farmer living in the area. "We were told to stay away from this area, not to go near it, that it was a security zone."
A few miles away, U.S. Marines guarded another site where two bodies and four bullet casing were found. A red keffiyah could be seen wrapped around the eyes of one of the skulls.
"This is the tip of the iceberg in this country," said Marine Capt. Mike Urena.
About 50 miles to the northeast, in a field on the outskirts of the ancient city of Babylon, residents kept vigil Sunday at a suspected mass grave they linked to Saddam Hussein's government.
About 25 skulls — many arranged on blankets — sat in the sun as Iraqis mourned and tried to identify loved ones. About half of the skulls had been cut open meticulously with hacksaws.
Locals said government operatives would arrive at night, dig holes and bury bodies mixed with large amounts of trash. The area was off-limits under Saddam's regime, they said.
"This is our land, and the Iraqi government took it," said one man who identified himself only as the "father of Adnan." He and others said the government had been apparently trying to conceal the bodies by mixing the trash in.
Residents said the U.S. military visited the site Saturday and told people to stop digging. So on Sunday, women cried and men reminisced as they gazed at the bones at the field's edge.