The Tribunal of the Inquisition was established in Portugal in 1536. This paper deals with three aspects concerning medicine in sixteenth- and seventeenth-century Portugal: the institution and its members, the medical practitioners, and the books. On the one hand, doctors were necessary to carry out specific duties in the life of the Inquisition. On the other hand, a significant percentage of the victims of the Inquisition were medical professionals, the overwhelming majority being New Christians accused of Judaism. Finally, as did the Roman and Spanish Inquisitions, the Portuguese Holy Office looked after the censorship of books, many of which dealt with medical matters.