Pipestone National Monument's collections include over 54,000 items. The collection includes archival documents and photographs, artifacts including tools, potshards, leather, pipes, and pipestone objects, and a broad collection of natural history specimens including insects and plants.

Selected pipes, pipestems, and other crafts are on display in the visitor center.  These items reflect the breadth of styles of pipes made by different cultures and in different periods.  Also on display in the visitor center are petroglyphs carved into blocks of quartzite.

Portions of the Pipestone National Monument collections are at the Midwest Archaeological Center in Lincoln, Nebraska.