The Native American boarding school system was vast and entrenched, ranging from small shacks in remote Alaskan outposts to refurbished military barracks in the Deep South to large institutions up and down both the West and East coasts.

Until recently, incomplete records and scant federal attention kept even the number of schools — let alone more details about how they functioned — unknown. The 523 schools represented here comprise the most comprehensive accounting to date of institutions involved in the system. This data was compiled over the course of several years by the National Native American Boarding School Healing Coalition, a nonprofit advocacy and research organization. It reflects the efforts of historians, researchers, activists and survivors who have filled in many of the blanks in this dark chapter of American history.

The first school opened in 1801, and hundreds were eventually established or supported by federal agencies such as the Interior Department and the Defense Department. Congress enacted laws to coerce Native American parents to send their children to the schools, including authorizing Interior Department officials to withhold treaty-guaranteed food rations to families who resisted.

Congress also funded schools through annual appropriations and with money from the sale of lands held by tribes. In addition, the government hired Roman Catholic, Presbyterian, Episcopalian and Congregationalist associations to run schools, regardless of whether they had experience in education, paying them an amount for each student.

Beyond the vast federal system, this new list also sheds light on boarding schools that operated without federal support. Religious organizations ran at least 105 schools; many were Catholic, Presbyterian or Episcopalian, but smaller congregations such as the Quakers ran schools of their own.

Wherever they were located or whoever ran them, the schools largely shared the mission of assimilating Indigenous students by erasing their culture. Children’s hair was cut off; their clothes were burned; they were given new, English names and were required to attend Christian religious services; and they were forced to perform manual labor, both on school premises and on surrounding farms. Those who dared to keep speaking their ancestral languages or observing their religious practices were often beaten.

While the boarding school era might seem like distant history, aging survivors, many in their 70s and 80s, are striving to ensure the harm that was done is remembered.

Ben Sherman, a member of the Oglala Sioux Tribe who spent four years living at the Oglala Community School in Pine Ridge, S.D., said he placed the emergence of some of the worst abuses at Native American boarding schools with the sunset of the “shooting wars” waged by the United States government against Indigenous peoples in the last decades of the 19th century.

“The government was not done with war, so the next phase involved war against the children,” said Mr. Sherman, 83, a former aerospace engineer.

“Don’t try to tell me this wasn’t genocide,” added Mr. Sherman, who said in an interview that he had once run away from the school and walked nearly 50 miles trying get home. “They went after our language, our culture, our family ties, our land. They succeeded on almost every level.”

Some of the most enduring impacts of the schools involved trauma passed on from one generation to the next, Mr. Sherman said, explaining how his immediate family attended boarding schools for four generations. His great-grandmother, Lizzie Glode, was among the first group sent to a boarding school in Carlisle, Pa.

One of Ms. Glode’s sons, Mark, attended the Rapid City Indian Boarding School. The environment there was so harsh, Mr. Sherman said, that in 1910, when Mark was 17, he and three other boys ran away. They followed the railroad tracks south toward the Pine Ridge reservation.

At one point, Mr. Sherman said, Mark and another boy slept on the railroad track. A train rolled through, striking and killing the two boys.

While researchers say the known toll is still far from complete, there are at least hundreds of Native children who died while attending boarding schools. In site after site, children’s bodies were stuffed into graves without regard for the burial traditions of their families or their cultures.

In recent years, tribal nations around the United States have begun to use technologies like remote sensing surveys and ground-penetrating radar to scour locations for evidence of burial sites. In July, the Paiute Indian Tribe of Utah confirmed that 12 children were buried in unmarked graves at the site of the Panguitch Indian Boarding School in southern Utah.

Archival records, including an 1899 map, make reference to a cemetery on the premises of Genoa Indian Industrial School in Nebraska, about 90 miles west of Omaha — but the location of the cemetery has been lost. At least 86 students are thought to have died at Genoa from causes including typhoid, tuberculosis and an accidental shooting.

Present-day investigation efforts to find students’ remains at Genoa are being led by the Nebraska state archaeologist, in consultation with 40 Native nations whose children attended the school.

In its preliminary report released last year, the Interior Department indicated it expected the number of children known to have died in Native American boarding schools to grow into “the thousands or tens of thousands.”

A driving force behind the frenetic expansion of the boarding school system was Richard Henry Pratt, a military officer who fought in the Red River War, a campaign in the 1870s to forcibly remove the Comanche, Kiowa and other tribes from the Southern Plains of the United States.

In 1879, Mr. Pratt founded the Carlisle Indian Industrial School, in what had been army barracks in Carlisle, Pa., and set about transforming it into a flagship institution spawning dozens of similar schools around the United States. He was blunt about his mission, as in an infamous proclamation: “Kill the Indian in him, and save the man.”

Mr. Pratt dreamed of abolishing the reservations and scattering the entire population of Native children across the country, with some 70,000 white families each taking in one Native American child. He came up short in this effort, but he did succeed in creating a model that placed schools in white communities, often far from the reservations where Native children were born.

Upon arriving at Mr. Pratt’s school, the children were often photographed in their Native clothing. Then the boys quickly had their long hair cut short, a particularly cruel and traumatic step for those coming from cultures like the Lakota, where the severing of long hair could be associated with mourning the dead.

Boarding schools made the assault on tribal identity a central feature of their assimilating mission, often starting with renaming children, as the historian David Wallace Adams explained in his 1995 book “Education for Extinction.”

One former Carlisle student, Luther Standing Bear, of the Rosebud Sioux Tribe and Oglala Lakota Nation, recalled being asked to point to one of the names written on a blackboard, then having the name written on a piece of tape and placed on the back of his shirt.

“When my turn came, I took a pointer and acted as if I were about to touch an enemy,” he wrote in “My Indian Boyhood,” his 1931 memoir. “Soon we all had the names of white men sewed on our backs.”

Just as Carlisle had a renaming policy, other schools took note, often assigning names that could be humiliating, such as Mary Swollen Face or Roy Bad Teeth. In other cases, children were randomly bestowed common American surnames like Smith, Brown or Clark, or given the names of presidents, vice presidents or other prominent figures.

Mr. Pratt’s photographers would take pictures of the children again — boys in their uniforms, girls in Victorian-style dresses — as evidence of the school’s mission.

Mr. Pratt imbued Carlisle with a militaristic culture, dressing and drilling the children as if they were soldiers and even using a court-martial format, in which older children would sit as judges over younger children, to enforce rules. (Mr. Pratt reserved the power to overrule the court.)

News of Mr. Pratt’s experiment spread, and a vast array of similar schools were established all over the country. Some of the clearest descriptions of what such schools sought to accomplish are relayed in the words of the white officials in charge of these institutions.

“It’s cheaper to educate Indians than to kill them,” Thomas J. Morgan, the commissioner of Indian affairs, said in a speech at the establishment of the Phoenix Indian School in 1891.

The same year, a newspaper report published an exchange between the superintendent of Grand Junction Indian School and the secretary of the Interior that indicated that a student’s toe was cut off because his foot could not fit into a government-issued shoe.

At Carlisle, authorities introduced an “outing” program: an arrangement by which children worked as manual laborers or maids in surrounding farms; businesses like wagon-makers; and households. The objective appeared to be to provide the students with a modest income while promoting practices of thrift and savings.

Other institutions made the access to a reservoir of cheap child laborers a selling point when persuading community leaders to establish a Native boarding school.

Such “outing” systems eventually became widespread around the United States. Practices differed considerably from school to school, and abuses emerged — such as paying the children unfair wages, making them cover their own room and board, removing them from their studies for months at a time, and placing them in lodgings that were substandard or segregated from white laborers.

In November 1894, U.S. soldiers arrived in the remote northern Arizona mesas where the Hopi people had lived since time immemorial. Their orders: Take the children.

But some Hopi parents had already made it clear they would not send their children to the Keams Canyon Boarding School. Facing resistance, authorities had tried bribing Hopi parents with yards of cloth, or tools like axes. They used their bare fists, striking Hopi who didn’t want to send their children away. They withheld food supplies guaranteed by treaties in a bid to starve the Hopi into submission.

When even those tactics failed, and resistance to having their children hauled away was compounded by tensions over farmland, two cavalry companies arrived to arrest 19 Hopi men. The captives were imprisoned on California’s Alcatraz Island for nearly a year, and the removal of Hopi children proceeded as planned.

The treatment of the Hopi, which briefly captured public attention in the 1890s when the writer Charles Lummis made it the focus of a crusade against federal Native American education policies, soon faded from view.

Brenda Child, a historian whose Ojibwe grandparents were sent to Native boarding schools, emphasized in an interview that the period of the greatest expansion of the boarding school system — from the last decades of the 19th century to the first decades of the 20th — coincided with colossal theft of Indigenous land.

When Native American boarding schools were opening at a steady clip around the country, the General Allotment Act of 1887 allowed federal authorities to divide up and distribute Native lands. The law effectively turbocharged land dispossession, allowing white people to take control of “surplus” land belonging to Indigenous peoples.

“Indian people lost 90 million acres of land during the half century that assimilation policy dominated Indian education in the United States,” said Dr. Child, a professor of American studies at the University of Minnesota.

Some of the earliest schools, like the Asbury Manual Labor School, near Fort Mitchell, Ala., took root in the 1820s, when the U.S. government was on the cusp of forcibly relocating peoples, including the Cherokee and Creek, from their homelands in the Southeast United States to lands west of the Mississippi River.

The Interior Department report released last year by Bryan Newland, the department’s assistant secretary for Indian affairs, showed that land dispossession and funding for Native American boarding schools went hand in hand. To help pay for the federal boarding school system, the inquiry noted, the federal government had used money from trust accounts set aside for the benefit of tribal nations as part of treaties in which they ceded lands to the United States. In other words, the United States government effectively made Indigenous peoples use their own funds to pay for boarding schools that severed their children’s ties to their families and cultures.

By the 1920s, so many Native American boarding schools had been created that nearly 83 percent of school-age Indigenous children were enrolled in such institutions.

Questions about the costs and effectiveness of assimilation policies, along with revelations of some of the horrors in the system, slowly led to changes. An inquiry in 1928, commonly known as the Meriam Report, detailed how children were malnourished, overworked and harshly disciplined.

In the 1930s, when the process of dispossessing Native lands had largely been completed, the federal government began shutting down many of the schools. That took decades, as Native peoples sought to gain control of the education of their own children, against a backdrop of activism aiming to bolster Native sovereignty.

From the 1960s to 1980s, federal authorities began handing over administration of some remaining schools to the Bureau of Indian Education or the tribes. Institutions such as the Santa Fe Indian School and the Sherman Indian High School, in Riverside, Calif., still operate under this model, emphasizing Native sovereignty and preserving traditional languages and cultures. At least nine boarding schools in the accounting of 523 schools opened after 1969.

A U.S. Senate report in 1969 noted the tragedy and failure of the system, helping to spur approval of the Indian Self-Determination and Education Assistance Act in 1975, giving tribal nations greater control over the schools.

A Supreme Court case this year reflected how the abuses of the boarding school era are still echoing across institutions. The case involved a challenge to a 1978 law, known as the Indian Child Welfare Act, aimed at keeping Native American adoptees within tribes. The court upheld the law, bolstering the notion that tribal nations are distinct sovereign communities in the United States and alleviating fears of resurrecting policies giving authorities greater power to separate Native children from their families and cultures.

Last year’s Interior Department investigation came at the direction of Secretary Deb Haaland, a member of the Laguna Pueblo whose own grandparents were boarding school survivors. In an effort to lift the veil on abuses within the system, Secretary Haaland has been traveling around the country for more than a year, conducting listening sessions with Indigenous communities still dealing with the fallout from the boarding school system. In the Senate, a bill has been introduced to establish a truth and healing commission to address the legacy of Native boarding schools, similar to one undertaken by the Canadian government in 2007.

“Federal Indian boarding school policies have impacted every Indigenous person I know,” Ms. Haaland said in a statement. “Some are survivors, some are descendants, but we all carry this painful legacy in our hearts and the trauma that these policies and these places have inflicted.”

Among the most far-reaching effects of the boarding school era was the way it molded Native children to feed into the American military and economy. Schools around the country trained Indigenous students to become manual laborers or prepared them to go to war — not against the United States, as some of their parents had done, but for it.

At the Phoenix Indian School, administrators developed an exceptionally militaristic atmosphere. In addition to requiring students to wear uniforms and conduct regular drills, all pupils had to stand for inspection at 7:30 a.m. on Sundays.

“Too much praise cannot be given to the merits of military organization, drill and routine in connection with the discipline of the school,” the school’s superintendent, Harwood Hall, wrote in an 1897 report.

A company of boys, trained by the Arizona National Guard, formed an elite campus group that was eventually attached to the 158th Infantry. When the United States entered World War I in 1917, the federal government had yet to recognize Native Americans as citizens, much less allow them to vote. But the Phoenix Indian School sent dozens of students to enlist during World War I. Two were killed.

In addition to training soldiers, the boarding schools sought to supply laborers. The Albuquerque Indian School, for instance, was known for sending boys out to work for local farmers, in addition to teaching “harness making, shoe making, cooking and baking, sewing, and laundry work,” according to a superintendent’s report in the 1890s.

But sometimes administrators looked much farther afield to place the children in their care into jobs. In 1905 and 1906, the Albuquerque Indian School sent 100 boys and 14 girls to work in Colorado, on the railroad and in the beet fields.

At Carlisle, which had pioneered the “outing” system, it soon became a brisk business. In one 18-month period beginning in March 1899, school records show more than 1,280 outings by about 900 students. Many students were sent out more than once, and at least 23 did not return to the school because they ran away from their outings. The map below shows more than 200 of their destinations, spanning five states and Washington, D.C.

Anita Yellowhair, 84, a Navajo survivor who was taken from her family in Steamboat, Ariz., to live at the Intermountain Indian School in Brigham City, Utah, said children were simply not allowed to question being made to work as part of their school experience.

“It was just what you did, no questions asked,” said Ms. Yellowhair, a former dental assistant who now lives in the Phoenix area. “They hired me out on weekends to clean the homes of white families.”

The Sherman Institute in Southern California made use of child labor from its very beginning in 1902 — starting with the construction of the school itself. Male students at the school built much of the institution intended to assimilate them into white culture: its dormitories, hospital, vocational workshops, farm buildings and auditorium.

The outing system at Sherman, which Kevin Whalen, a historian, called “a means to prepare students for second-class existence,” became known for sending so many girls to work as servants in white households that the school employed an “outing matron” to supervise them.

Sherman also sent boys to labor in fields around Southern California, picking citrus fruit, digging ditches, managing livestock and cutting and baling hay. One company, Fontana Farms, employed hundreds of male students, mostly Navajo and Hopi, from 1908 to 1929, making them work six days a week for 10 hours a day and live in racially segregated shacks apart from white workers.

James LaBelle was 8 years old in 1955, when he was taken with his 6-year-old brother to the airport in Fairbanks, Alaska. He said his mother, who struggled with alcoholism, had been given a choice: send her sons to boarding school or put them up for adoption.

When his mother chose boarding school, Mr. LaBelle said, he found himself literally tied to other Native Alaskan children by a rope inserted in the belt loops of their pants. He said his destination, where he spent the next several years, was the Wrangell Institute, a boarding school operated by the Bureau of Indian Affairs in southeast Alaska.

Mr. LaBelle, who is Inupiaq and an enrolled member of the Native Village of Port Graham, still finds it hard to describe the treatment he endured at Wrangell. Now 76, his voice grows shaky when he recounts the punishments children received — and how children were turned into punishers.

During weekdays, it was common for supervisors to tell children to undress so they could be paddled or whipped with a cat-o’-nine-tails, Mr. LaBelle said. And when weekends came, he said, it was time for the “gauntlet,” when some children were ordered to get completely naked and others were ordered to hit them with belts for perceived violations of school rules.

“It could have been a prison or a mental hospital,” said Mr. LaBelle, who is now a lecturer on historical trauma and a board member of the National Native American Boarding School Healing Coalition. “They made the children the enforcers.”

When he was 10, Mr. LaBelle said, he and another boy were punished for wrestling by being doused with nearly freezing water from a fire hose. Sexual violence was also rampant, he said, citing the example of a girl who was repeatedly abused by an administrator for the entire eight years she was at Wrangell.

And in addition to witnessing other male students being raped by a supervisor, Mr. LaBelle said, he was sodomized by another boy. When the lights went out at night, Mr. LaBelle said, he could hear other children, especially some of the youngest, sobbing and calling for their mothers.

“It was the only time we could show emotion,” Mr. LaBelle said. “It didn’t take very long until it grew and grew and grew. The entire section of the dorm for the youngest kids were all wailing in the dark.”

The range of experiences at these schools was immensely varied. Despite the overwhelming emphasis on assimilating children into the dominant white culture of the United States, some former students were exposed to Indigenous cultures different from their own, met their future spouses or learned a trade that enabled them to put food on their family’s table. But many survivors say the horrors of the system saturated their own experiences to the point where they linger with them to this day.

“I was just a child, so I couldn’t stand up for myself,” said Ms. Yellowhair, who described the punishment meted out at Utah’s Intermountain school to students caught speaking languages other than English. “For doing that, they made us get on our knees to clean the toilets,” Ms. Yellowhair added. “It was very embarrassing and humiliating. That’s why some of us never talk about our time at school.”

Ms. Yellowhair and Mr. LaBelle are among the survivors attempting to grapple with the trauma of the boarding school experience as it endures in their own bones and is passed on, metamorphosing and evolving into different forms of grief, from one generation to the next. They have chosen to make their own painful experiences public; others do not.

Public health researchers have begun to attempt to account for the lasting toll of boarding school attendance, as well. A study by Ursula Running Bear of the University of North Dakota found that Native Americans who had attended boarding school were more likely to have a host of serious chronic health conditions than Native people who did not attend boarding school, even after controlling for demographic factors. Her work builds on similar findings concerning the Indigenous residential school system in Canada.

While it may be impossible to fully recount the horrors of the time, some of the most devastating and harrowing episodes were laid out in routine bureaucratic reports, which listed the toll of dead children as if they were discussing livestock losses.

For instance, several paragraphs into a subsection of the “Report Concerning Indians in Utah” submitted in July 1901 to the Interior Department, E.O. Hughes, the superintendent of the Uintah Boarding School in Whiterocks, Utah, noted that something unusual had happened.

“In December came the catastrophe,” Mr. Hughes said in his report. A measles outbreak that started at the boarding school, he explained, quickly spread to more than half the school because of substandard care in the infirmary. Learning of the crisis, many parents from surrounding reservations quickly went to the Uintah school and took their children home.

“It was found necessary to call for a troop of cavalry to protect the buildings from being burned,” Mr. Hughes wrote, noting that “four of our pupils died in camp,” while another 17 children in the vicinity died as a result of the measles outbreak.

A precise accounting of how many children died at Native American boarding schools remains elusive. At some schools, dozens of children died; 189 students are known to be buried at Carlisle alone. Clues continue to emerge.

For instance, in a city park just north of downtown Albuquerque, workers digging irrigation trenches in the 1970s found the bones of children. The site, it turned out, was the cemetery of the Albuquerque Indian School.

A decades-old plaque describing the location as “used primarily for burial of Albuquerque Indian School students from the Zuñi, Navajo and Apache tribes” itself went largely unnoticed until the discoveries of student graves at Canadian boarding schools recently focused greater attention on such sites in the United States.

Now the plaque is gone, replaced by a memorial under the shade of a tree with stuffed animals, toys and an old basketball. A sticker on a weathered sign at the memorial proclaims “Land Back” — a slogan of a movement seeking to re-establish Indigenous sovereignty over purloined lands.

Plastic mesh fencing around the site seeks to place it off limits to any further despoiling. And another sign, this one put up by the City of Albuquerque, warns passersby that disturbing marked burial grounds can result in a felony charge. On a recent day in late July, the entire park, including the area where Native children were once laid to rest, was empty.

Reflecting how the reckoning of the boarding school era is still in an incipient phase, in Albuquerque and around the United States, the sign explains that the city is “listening to Pueblo & Tribal Leaders, as well as the broader community, to plan the future of this site.”