Formerly known as the Gabinetto di Anatomia Fisiologica, and then as the Museo di Anatomia Normale della Regia Università di Siena, the Museum originated from the collection of the famous anatomist Paolo Mascagni. Later, in 1862, it was assigned new spaces and funds by the directors of the Hospital of Santa Maria della Scala, and was thus able to increment its anatomic and histologic specimens. Since April 2001 the Museum, under the management of the University of Siena Department of Anatomical and Biomedical Sciences, has occupied new premises at the University's Biological Institutes.

Its historic collection, dating mainly from the 19th century, includes wax anatomical models, a collection of skulls and foetuses. Particularly interesting is the collection of numerous dried anatomical specimens, them some prepared by Paolo Mascagni. The Museum also has an educational collection consisting of nineteenth-twentieth century models of lymphatic angiology and an ample collection of plates with anatomical drawings. Some of the rooms are arranged as reconstructions of dissection theatres, laboratories and study environments, as catalogued in 1865.