Hunter was an influential figure who built up large natural history collections, amongst which minerals predominated. He was not a mere collector, however, and both his library and collections were sought out by contemporary workers.
Analytical mineralogy only emerged from its alchemical background towards the end of Hunter's lifetime, and his library contains most of this early mineralogical literature, to some of which at least he was a subscriber. He also possessed a number of lapidaries, one of them a unique manuscript, and several specimens indicate his interest in medical mineralogy. The contents of Hunter's mineral and rock collections reflect the interests of his day: there is a piece of the Siberian iron mass which was only accepted as a meteorite in 1794, after Hunter's death, and lavas from Vesuvius, together with his subscription copy of Hamilton's classic 1776 study of that volcano. Lavas from Iceland - perhaps from Sir Joseph Banks - reflect the Plutonist - Neptunist debate, and Hunter's museum was also visited by Raspe, the German Neptunist.
Hunter (1768) was the first to establish, on comparative morphological grounds, that the American mastodon differed from living elephants, and that it must therefore be extinct - an idea with which Buffon had toyed in 1761. A recently published manuscript of 1770-1773 shows that Hunter realised the Irish ‘elk’ was quite different from the living American moose, contrary to the then current opinion, and that it too must be extinct. It was to be another forty years before Cuvier demonstrated this difference in comparable detail. Hunter thus broke the Great Chain of Being twice, at the high level of quadrupeds, only one down the ladder of life from man and monkey. This was an important contribution to Enlightenment thought, since "one step broken, the great scale's destroyed" (Pope, 1733).
Hunter acquired the foremost collection of Recent corals in Europe, on Fothergill's death in 1781. Corals not only linked inert with living parts of the Chain of Being but, with newly discovered coral islands, formed part of Whitehurst's 1778 theory of the Earth for constructing land.
Between 1764 and 1778, Hunter commissioned many drawings of bodily concretions, which were primarily of medical concern. Hunter may also have had an interest in them as part of the ‘stoniness’ problem, for the light they might shed on the fossilisation question.