For more than a century, from the late 1870s to the early 1970s, the U.S. government forcibly took thousands of Native American children from reservations and sent them to federal or religious boarding schools. At that time, supporters of the policy said these institutions would help Indians assimilate into mainstream American society, while later critics charged that the schools tried to eradicate the Indian culture by suppressing traditional languages and customs.

Now, there's a new criticism of the system: a multi-billion dollar lawsuit accusing the government of neglecting its treaty-bound duty to protect tribes from "bad men among the whites" during the boarding school era. Attorneys said many Indian students were physically, mentally, or sexually abused by staff. The first three schools named in the suit are Catholic, compounding the problems the Church already faces from last year's barrage of abuse allegations against priests.

At his home near Wagner, South Dakota, Sherwin Zephier organizes his art supplies and papers. The Yankton Sioux tribal member teaches art in the nearby town of Marty. The tribal school sits across from the former campus of a Catholic boarding school called St. Paul's, which operated until 1976, when the property was transferred to the tribe. Mr. Zephier was a student there from 1963 to 1975, and recalls how he and his peers were disciplined by the nuns and priests. He said, "We were beaten frequently, not just spanked. With boards, whips, leather straps like the shaving blade sharpeners, real thick leather. Sometimes two were put together to thicken it, to increase pain or impact of it. For some of us, when we were whipped, it broke skin, left scars."

Mr. Zephier said he doesn't know why he was beaten often, except that he and his friends usually conversed in Lakota while on the playground. Students at St. Paul's like those at the other Indian boarding schools were forbidden to speak anything other than English. Mr. Zephier is one of several Native Americans in South Dakota who are part of a lawsuit against the U.S. government, for alleged abuses through the boarding school system. Since the suit was filed in April, numerous other accounts have surfaced alleging torture, neglect, and other atrocities. The St. Francis boarding school on the Rosebud Sioux Reservation is singled out in a charge by Sonny One Star, who said he was sexually molested by a nun while he was a first grader there.

Los Angeles legal consultant Gary Frischer said "Sonny One Star's one of most courageous people I've ever met." He said the lawsuit represents about 1,000 plaintiffs. But by next year, he expects that number to grow to 25,000, thanks to those, like Sonny One Star, who've stepped forward.

"To explain what happened in his youth to the world, and his place on the reservation takes a lot courage. He's a full-blood, a hereditary chief. He's a leader of his people. That's why I thank Sonny because he's led the way for others," he said.

Federal officials have declined comment on the case, until it's heard in court. But some administrators associated with the now defunct boarding schools have chosen to speak openly on the matter.

Here on the campus of what used to be the St. Francis Boarding School, Indian children ride their bikes between the steepled church and the administrative offices, while maintenance crews work in the garage. Mary Van Winkel is Executive Director of St. Francis Mission, which now operates a museum, radio station, and parish, plus several youth programs and a tribal employment service. She said administrators are receptive to complaints from boarding school alumni.

"The St. Francis mission/Rosebud School system takes all allegations seriously, and we encourage anyone who thinks they've been harmed to report such activities to the proper authorities, and hopefully someone here so that proper pastoral care can be given to that individual," Ms. Van Winkel said.

The Wisconsin Province Society of Jesuits, which sponsors St. Francis, said it has launched its own investigation into the matter. Officials said some claims will be difficult to follow up on, as several alleged perpetrators are deceased.

The lawsuit has cast an even darker shadow on the Indian boarding school system, which many Native American activists have condemned as a government tool for eradicating traditional Indian singing, dancing, language, and dress.

But some graduates have defended their alma mater. Patrick Lee, an Oglala Sioux tribal member and former judge, attended Holy Rosary on the Pine Ridge Reservation in the 1940s.

"For me and my family it was positive. My parents and many of my relatives' parents, related well to each mission. During the 40s poverty was rampant on the reservation, and it was a relief for parents to put us in a place where we were educated, had 3 square meals. And I value the religious training I got there as well as academics," Mr. Lee said.

Mr. Lee said while problem students were spanked with a belt or given demerits, he never saw or heard of any sexual abuse or torture of his classmates. He said if the allegations are true, he sympathizes with the victims, but he wants the positive aspects of the boarding school system to be known as well.

In the meantime, the lawsuit is gaining momentum across the United States. Gary Frischer said complaints have come from Alaska, South Dakota, California, and New York, with more to follow. He said in time, individual churches and offenders will be listed. The plaintiffs are asking for $25 billion in damages for the emotional and physical injuries they said they suffered under the government's boarding school policy.