Now, a new discovery offers chilling evidence that many of the missing children may have died at these schools: The remains of as many as 751 people, mainly Indigenous children, were found at the site of a former school in the province of Saskatchewan, an Indigenous group said on Thursday.
The burial site, the largest one to date, was uncovered only weeks after the remains of 215 children were found in unmarked graves on the grounds of another former church-run school for Indigenous students in British Columbia.
The discoveries have jolted a nation grappling with generations of widespread and systematic abuse of Indigenous people, many of whom are survivors of the boarding schools. For decades, they suggested through their oral histories that thousands of children disappeared from the schools, but they were often met with skepticism. The revelations of two unmarked grave sites are another searing reminder of this traumatic period in history. Continue reading from New York Times
Since then, more unmarked gravesites have been found, providing previews of investigations by Canada's First Nations into the deaths of residential school students.
A rising tally of these graves - more than 1,100 so far - has triggered a national reckoning over Canada's legacy of residential schools. These government-funded boarding schools were part of the policy to attempt to assimilate Indigenous children and destroy Indigenous cultures and languages.
Here's what we know about the findings so far.
What do we know about the 215 graves?
In May, Tk'emlúps te Secwépemc Chief Rosanne Casimir announced that the remains of 215 children had been found near the city of Kamloops in southern British Columbia (BC) as part of a preliminary investigation.
Some of remains are believed to be of children as young as three.
All of the children are believed to have been students at the Kamloops Indian Residential School - the largest such institution in Canada's residential school system.
The remains had been confirmed with the help of ground-penetrating radar technology, Chief Casimir said, following preliminary work on identifying the burial sites in the early 2000s.
The full report into the remains found is due on Thursday, and the earlier findings may be revised. Indigenous leaders and advocates have said they expect the 215 figure to rise.
"Regrettably, we know that many more children are unaccounted for," said Chief Casimir in a statement.
Thousands of children died in residential schools and their bodies rarely returned home. Many were buried in neglected graves.
To this day there is no full picture of the number of children who died in residential schools, the circumstances of their deaths, or where they are buried. Efforts like those of the Tk'emlúps te Secwépemc First Nation and others are helping to piece some of that history together.
The Kamloops school, which operated between 1890 and 1969, held up to 500 Indigenous students at any one time, many sent to live at the school hundreds of kilometers from their families. Between 1969 and 1978, it was used as a residence for students attending local day schools.
Of the remains found, 50 children are believed to have already been identified, said Stephanie Scott, executive director of the National Centre for Truth and Reconciliation. Their deaths, where known, range from 1900 to 1971.
But for the other 165, there are no available records to mark their identities. Children "ended up in pauper graves," Ms. Scott said. "Unmarked, unknown."
What about the other sites?
In June, the Cowessess First Nation in Saskatchewan announced it had found an estimated 751 unmarked graves after a similar investigation - the largest such discovery to date. The remains were found near the former Marieval Indian Residential School, which operated from 1899 to the 1990s and was under the control of the Roman Catholic Church for much of that time.
Cowessess leaders have not yet determined if all the unmarked graves belonging to former students. Technical teams will continue the investigation to provide verified numbers.
Cowessess Chief Cadmus Delorme emphasized that the discovery was of unmarked graves - not a mass grave site - and suggested that the Catholic Church may have removed grave markers at some point in the 1960s.
A week later, the Lower Kootenay Band in British Columbia said the remains of an additional 182 people had been found near the grounds of the former St Eugene's Mission School. St Eugene's was operated by the Catholic Church from 1912 until the early 1970s. Continue reading from BBC