In 1768 he built the famous anatomy theatre and museum in Great Windmill Street, Soho, where the best British anatomists and surgeons of the period were trained.

His greatest work was Anatomia uteri umani gravidi [The anatomy of the human gravid uterus exhibited in figures] (1774), with plates engraved by Rymsdyk (1730–90),[4] and published by the Baskerville Press.

[5] To aid his teaching of dissection, in 1775 Hunter commissioned sculptor Agostino Carlini to make a cast of the flayed but muscular corpse of a recently executed criminal, a smuggler.

Around 1765 William Hunter started collecting widely across a range of themes beyond medicine and anatomy: books, manuscripts, prints, coins, shells, zoological specimens, and minerals.

In 2010, the self-described historian[7] Don Shelton made some lurid claims about the methods by which Hunter, his brother John, and his teacher and competitor William Smellie might have obtained bodies for their anatomical work.

In a non-peer-reviewed opinion piece in the Journal of the Royal Society of Medicine he suggested that the two physicians committed multiple murders of pregnant women in order to gain access to corpses for anatomical dissection and physiological experimentation.

[9][10] Shelton's comments attracted media publicity, but were heavily criticised on factual and methodological grounds by medical historians, who pointed out that in 1761, Peter Camper had indicated that figures "were not all from real life",[11] and likely methods other than murder were available to obtain bodies of recently deceased pregnant women at that time.

[14] That "multiple methods of preservation were combined" at Hunter's Great Windmill Street school in order to retain as much information from the individual cadavers as possible further indicates the rarity and value of these bodies.