The museum's zoological collections were developed by A.C. Shelton, University of Oregon field collector, during the early 20th century.
The collections were expanded in the 1920s with A.G. Prill’s ornithological collections. Featuring a diverse sample of modern animals from Oregon, the collections are used for comparison and identification of specimens from cultural and paleontological sites, for teaching, and in museum exhibits.
The collection includes numerous bird specimens such as skins, skulls, mounted specimens, eggs, and nests. The bird collections come primarily from Oregon.
The collection also contains numerous comparative skeletons including birds, mammals, reptiles, amphibians, and fish. The museum's Grand Comparative Primate Collection, curated by UO primatologist Frances White, is a part of this collection. It also contains a sizable assemblage of invertebrates including snails, chambered nautilus, bivalves, corals, arthropods, and echinoderms like sea urchins, sea biscuits, and sand dollars.