Since the Middle Ages, ecclesiastical authorities considered medical activity worthy of their attention and control. During the Counter-Reformation, they toughened their disciplinary action, aware of the peculiarity of an ars that mixed together the cure of the body with the cure of the soul. Moreover, the authorities became increasingly suspicious of practitioners who were highly involved in the Reformation movement, and who distanced themselves from Catholicism in the epistemological premises of their work. By examining original sources from the Venetian Inquisition archive, this paper discusses the factors that put the Roman Church and the medical profession in opposition to each other in the sixteenth century, and describes the professional solidarity put forward by physicians. It also examines the problematic relationship between doctors and the Inquisition, dealing with the former as effective agents of heretical propaganda.