A medicinal herb garden proves to have been active in Siena at the Santa Maria della Scala Hospital as of the late 16th century. In 1784, twenty-five years after the transformation of the Chair of Medicinal Herbs into the Chair of Natural History, the Botanical Garden of the University was instituted at the Hospital, and in 1856 transferred to its current location, near the Accademia dei Fisiocritici, continuing to be enlarged and transformed through the years.

The outdoor collection of plants includes numerous specimens systematically arranged, old specimens of exotic plants which testify to the nineteenth-century layout, and varyingly arranged indigenous plants. The greenhouse plants are housed in various structures: the hothouse built in the late 19th century by Attilio Tassi (director from 1860 to 1905), houses species from tropical zones; the tepidarium, used to house the exotic species in winter, has a section devoted to succulent plants cultivated on the ground and distinguished according to their country of origin; the lemon-house contains showcases with insectivorous plants, the collection of the main citrus trees cultivated in Europe, and the species utilised in experimental studies. Fruit-bearing trees, olive trees and grapevines, including the principle grapevines of Chianti, are also cultivated. This section of the Garden is currently being subjected to transformations to set up the new collections.