The collection of the MMBM includes books from the first decade of book printing up through the 20th century and archive material. The inventory is housed in specially secured and air-conditioned archives and is professionally restored as needed.
The library focuses on the following subjects: medicine (anatomy, surgery and herbal medicine, including alchemy), natural history and botany, the theory of evolution and the history of medicine. In addition to valuable, partly old coloured originals, the library also contains later reprints and research literature from the 20th century. The collection is further expanded as needed. Handwritten documents and graphics originating from private donations are available in the archives.
The private library of the physician and medical historian Gustav Adolf Wehrli (1888–1949) forms the basis of the collection. Dr. Franz Käppeli was able to buy the Private Collection in its entity at an auction in 2010. Ever since he acquires particularly interesting and rare works on medical and natural history.