This article examines the practice of post-mortem examination in the Royal Navy during the French Revolutionary and Napoleonic Wars (1793–1815). The professional medical logbooks kept by ship’s surgeons as part of their mandated practice reveal that they turned to pathological anatomy to diagnose their patients – a technique typically associated with French anatomy during this period. I show that these post-mortem dissections blended medicine and surgery together by correlating clinical signs and symptoms of disease with pathological manifestations of disease in the bodies after death. This article also considers the medical culture that existed on these ships that enabled this research, specifically how captains, officers and crew responded to, and interpreted, such medical enquiry on board. By resituating the naval ship as a site of medical experimentation and enquiry, I explore how naval surgeons participated in medical research within the Royal Navy and used the ship space to engage in pathological anatomy before their British civilian counterparts flocked to French hospitals after the wars.