The Bureau of American Ethnology (or BAE, originally, Bureau of Ethnology) was established in 1879 by an act of Congress for the purpose of transferring archives, records and materials relating to the Indians of North America from the Interior Department to the Smithsonian Institution. But from the start, the bureau's visionary founding director, John Wesley Powell, promoted a broader mission: "to organize anthropologic research in America." Under Powell, the bureau organized research-intensive multi-year projects; sponsored ethnographic, archaeological and linguistic field research; initiated publications series (most notably its Annual Reports and Bulletins); and promoted the fledgling discipline of anthropology. It prepared exhibits for expositions and collected anthropological artifacts for the Smithsonian United States National Museum. In addition, the BAE was the official repository of documents concerning American Indians collected by the various US geological surveys, especially the Geographical and Geological Survey of the Rocky Mountain Region and the Geological Survey of the Territories. It developed a manuscript repository, library and illustrations section that included photographic work and the collection of photographs.

In 1897, the Bureau of Ethnology's name changed to the Bureau of American Ethnology (BAE) to emphasize the geographic limit of its interests, although its staff briefly conducted research in US possessions such as Hawaii and the Philippines. In 1965, the BAE merged with the Smithsonian's Department of Anthropology to form the Smithsonian Office of Anthropology within the United States National Museum (now the Department of Anthropology, National Museum of Natural History). In 1968, the SOA archives became the National Anthropological Archives.