- Boone County Historical Society
Includes the Walters-Boone County Historical Museum and Visitors Center, Boone Junction History Village and the Maplewood historic home.
- Enns Entomology Museum - UMC
- Museum of Art and Archaeology - UMC
- Museum of Anthropology - UMC
- American Jazz Museum – Kansas City
- Cole County Historical Museum – Jefferson City
- Missouri State Museum – Jefferson City
Located on the first floor of the Missouri State Capitol Building.
- Mark Twain Boyhood Home & Museum – Hannibal
- Kansas City Union Station
Houses a permanent rail exhibit, a science center, and more.
- Kemper Museum of Contemporary Art – Kansas City
- Museum of Westward Expansion
Housed in the Gateway Arch, St. Louis
- Negro Leagues Baseball Museum – Kansas City
- Nelson-Atkins Museum of Art – Kansas City
- St. Louis Art Museum
- St. Louis Science Center
- Steamboat Arabia Museum – Kansas City
- Missouri Art Museums
- Missouri Historical Museums
- Missouri Museums