During the early modern period, medical practitioners came to play an increasingly important role in criminal proceedings throughout continental Europe. Nevertheless, medico-legal procedures in the Southern or Habsburg Netherlands have hardly received any attention from historians of forensic medicine. The present article aims to address this issue by studying how suspicious deaths were investigated in the early modern County of Flanders. More specifically, three major aspects of the Flemish medico-legal death investigation system are analysed: the composition of the corps of medical practitioners on which the judicial authorities relied to conduct post-mortem examinations, the content of post-mortem reports, and arrangements for the remuneration of medical experts. Although surgeons initially constituted the principal group of medical examiners, university-trained physicians were increasingly required to participate in death investigations over the course of the seventeenth and eighteenth centuries. Furthermore, this period also witnessed a gradual increase in the number of internal autopsies. However, arrangements for the payment of medical experts remained largely unchanged throughout the early modern period.