American Indian School Records
The desire of many of those involved in Indian Affairs was to assimilate the native population and to teach them to rid themselves of their native culture. Efforts were made to accomplish that by sending representatives of various religious denominations to “convert them to Christianity.” Certainly, this effort was met with some success.
Another approach was tried in the late 1800s. Some felt that if the American Indian children could be sent to schools off the reservations, they could be taught to learn English and to renounce their culture. Lt. Richard Henry Pratt established the Carlisle Indian School in Pennsylvania, which became the beginning of the Indian Boarding School System.
An Education Division of the Bureau of Indian Affairs was established in 1885. This brought an intensification of the effort to educate the younger American Indians in agriculture, domestic skills, mechanical training, and the basic subjects of reading, writing, and arithmetic.
A number of boarding schools were established, all of which required the young person to leave their family, their reservation, and their culture to live at the school and be taught. Some of the more well-known boarding school include the Carlisle Indian School in Pennsylvania, Haskell Institute in Kansas, Sherman Institute in California, Chilocco School in Oklahoma, and the Intermountain Indian School in Utah. In all, there were some 500 boarding schools, some near the reservations they served, but many which were far away. Most of the boarding school had ceased to operate by the 1980s.
The agents of the Bureau of Indian Affairs on each reservation were required to maintain records of potential students at schools. School census records included names school-age children, their age, place of birth, and, in some cases, the name of their parent or guardian. Reports were sent by the agents to the Commissioner of Indian Affairs regarding the enrollment of students from their reservation.
The schools themselves maintained individual pupil files, as well as attendance records, and other records of the health of the students, teachers at the schools, etc.
The Reservation Boarding School System in the United States, 1870-1928. – 
Haskell Indian Nations University – 
Intermountain Indian School – 
Sherman Institute -- http://www.nps.gov/history/history/online_books/5views/5views1h82.htm