We study the impact of the Roman Inquisition on science during the Scientific Revolution of the 16th and 17th centuries. A structural model of occupation and location decisions enables the quantification of causal mechanisms and counterfactual historical experiments in a setting where a reduced-form approach is undermined by migration and knowledge spillovers. Using historical data on notable people, we find that the drivers of Italy's scientific decline since the 1540s are the Inquisition's deterrence effect -- which induced scientists to migrate, thus also discouraging talented individuals to engage in science in the first place -- and the training effect stemming from the consequent reduced availability of science masters. We conclude that the Roman Inquisition depressed scientific scholarship in the Italian peninsula by about 24% during the run-up to the Industrial Revolution. Owing to such migration and knowledge spillovers, this institution also had overall negative consequences for science in the rest of Europe. (with E.DeWitte, F.Drago and G.Zanella)