The Examen de ingenios para las sciencias, published in 1575 by the Spanish physician Juan Huarte de San Juan (1529/1530-1588), was a bold attempt to apply the principles of Galenic naturalism to a better understanding of human capabilities. Inevitably, the work also touched upon a number of theological issues, especially the delicate question of the interplay between natural abilities and supernatural gifts. When the treatise was included in the Portuguese Index of 1581, and then in the Spanish Indexes of 1583 and 1584, Huarte was allowed to amend some of his positions, as is evident in the second edition published posthumously in 1594. The aim of this article is to shed light on the identity of an ‘expurgated’ book by concentrating on some of the most significant changes in the Examen triggered by the intervention of the Spanish Inquisition. It will become apparent that Huarte’s response to censorship was not acquiescence or dissembling, but active engagement with the inquisitorial challenge.