In the 1690s the Roman Inquisition targeted medical circles, as they allegedly disseminated atheism under the veil of new explanations of the body. This article revisits these affairs, focussing on Rome. It argues that increased inquisitorial pressure must be set against the backdrop of struggles for hegemony in the papal curia, in which physicians were entangled. Notwithstanding such political vicissitudes, ecclesiastical control played a relevant role in shaping Italian medicine at the turn of the seventeenth and eighteenth centuries. The article suggests that the result may have been, paradoxically, a form of un-assumed materialism, though framed within the disciplinary borders of practical medicine, which enabled physicians to re-assert their autonomy.