It started as a Gabinete de Fisica, or observation room, of mineral, botanical and biological collections in the 17th century.

Ramon Martinez, O.P., a professor of natural history, founded the UST Museum of Arts and Sciences in 1871.

However, it was Casto de Elera, O.P., who started to systematically gather and catalogue all the collections, some of which date back to 1682.

Starting in 1941, the museum acquired the works of Filipino masters such as Fernando and Pablo Amorsolo, Carlos Francisco, Vicente Manansala, and Galo Ocampo.

The museum has permanent displays for specimens of natural history, ethnographic materials, Oriental art objects, Philippine religious images, paintings, and Coins, Medals, and Memorabilia.