As an 18th century collector, the anatomist William Hunter had a collection reflecting a diverse range of tastes and interests, including palaeontology. His credentials as a classic Scottish Enlightenment figure are most powerfully expressed in his writings advocating the fossil record as a source of evidence for extinction. This lends a peculiar significance to his own palaeontological material above all of his other collections - yet paradoxically this was one of the few collections to be neglected by his Trustees who failed to produce a catalogue of his fossil material when they audited his objects prior to their transportation to the University of Glasgow. This paper examines the evidence for work by a previous generation of palaeontological curators at the Hunterian Museum in attempting to retrospectively identify William Hunter's original specimens from within the broad range of material present in the 19th century that survives in today's collections.