The expedition commanded by the Frenchman Nicolas Thomas Baudin aboard the ships Le Géographe and Le Naturaliste (and Le Casuarina for the return journey) to the southern hemisphere between 1800-1804 collected specimens from numerous locations including the Canary Islands (Tenerife), Île de France (Mauritius), Cape Town (South Africa), Australia and Timor. Additionally, specimens were donated or purchased from locations not visited including the Comoros, Madagascar and Sumatra. Unfortunately, Baudin died at Île de France on the return trip so the responsibility of the account of the voyage was given to other members of the expedition. Responsibility for writing up the primary account of the voyage was granted to François Péron, who published the first volume of the narrative of the Voyage de Découvertes aux Terres Australes in 1807. Following his death in 1810, the second volume of the narrative was completed by Louis de Freycinet and published in 1816. The other four volumes of the Voyage included three atlases (the first by expedition artists Charles-Alexandre Lesueur and Nicolas-Martin Petit in 1807 and the second and third by Freycinet in 1811 and 1812), and a volume entitled Navigation et Géographie by Freycinet in 1815. Based on recent and on-going research, a review of many of the original documents is presented here, revealing hitherto unpublished details about who collected and donated mammals to the expedition. Research was conducted mainly in the collections of the Muséum national d'Histoire naturelle (MNHN) in Paris and their associated acquisition books. The Baudin expedition was responsible for an unprecedented collection of over 100 000 specimens of natural history, which remains the single largest collection of natural history specimens from Australia. A total of 101 mammal taxa relating to the Baudin expedition were identified during this study, which included 51 species described as a result of the expedition and 50 species that were described either before or subsequently, but not associated with the expedition. Of the taxa described, 20 species and three subspecies are currently recognised valid. During this study 43 museum specimens that were referable to 29 taxa were identified and at least five specimens seem to have been misplaced based on the information available. These specimens were derived from 24 holotypes, four paratypes, three syntypes, five lectotypes, and six paralectotypes and one topotype that are currently held at the MNHN. Some of these specimens are part of the estimated 51 mammals that were brought back alive to France on the boats. Charles-Alexandre Lesueur's illustrations complemented this study; of the 177 that are held at the Muséum d'Histoire naturelle du Havre, 149 could be attributed to one or more species and 28 were of unidentified species.