The Museum's anthropology collection consists of more than 8 million archaeological specimens and ethnographic objects, and is among the most extensive in the United States. It is housed at the Research and Collections Center in Springfield and the Dickson Mounds Museum in Lewistown.

Prehistoric artifacts from over 2,000 sites represent every period of Native American prehistory ranging in age from 12,000 years ago to about 300 years ago. Among the most important collections are those from Modoc Rock Shelter and Cahokia Mounds-one of only two U.S. sites on the prestigious United Nation's World Heritage List. The collection includes outstanding examples of stone tools, pottery, bone and shell tools and ornaments, and sculpted stone pipes.

The Historic-era collections consist of Native American and French colonial and nineteenth and twentieth-century Euro-American artifacts.

The ethnographic collections consist of 5,00 objects from cultures throughout the world. The largest holdings are late nineteenth to early twentieth century Native American baskets, textiles, ceramics, and apparel from the American Southwest, Northwest Coast, and Great Plains. Other major collections include the Frost Trade Bead Collection and the F. Louis Hoover African Collection from Illinois State University.