Medical factors including tuberculosis, scurvy, lead poisoning and botulism have been proposed to explain the high death rate prior to desertion of the ships on Sir John Franklin's expedition of 1845–1848 but their role remains unclear because the surgeons’ Sick books which recorded illness on board have eluded discovery. In their absence, this study examines the Sick books of Royal Naval search squadrons sent in search of Franklin, and which encountered similar conditions to his ships, to consider whether their morbidity and mortality might reflect that of the missing expedition. The Sick books of HMS Assistance, Enterprise, Intrepid, Investigator, Pioneer and Resolute yielded 1,480 cases that were coded for statistical analysis. On the basis of the squadrons’ patterns of illness it was concluded that Franklin's crews would have suffered common respiratory and gastro-intestinal disorders, injuries and exposure and that deaths might have occurred from respiratory, cardiovascular and tubercular conditions. Scurvy occurred commonly and it was shown that the method of preparing ‘antiscorbutic’ lemon juice for the search squadrons and Franklin's ships would have reduced its capacity to prevent the disease but there were no grounds to conclude that scurvy was significant at the time of deserting the ships. There was no clear evidence of lead poisoning despite the relatively high level of lead exposure that was inevitable on ships at that time. There was no significant difference between the deaths of non-officer ranks on Franklin's ships and several of the search ships. The greater number of deaths of Franklin's officers was proposed to be more probably a result of non-medical factors such as accidents and injuries sustained while hunting and during exploration.