Compared to workers on land, seamen working on the ocean are given only limited disease treatment. The aim of this paper is to clarify the actual condition of diseases among such seamen in an effort to improve measures that promote their health. We analyzed 51,641 cases of diseases that were reported to the Ministry of Land, Infrastructure and Transport from 1986 to 2000. The most prevalent diseases included disorders of the digestive system, followed by those of the musculoskeletal and the circulatory systems. The proportions of the three disease types were shown to vary by the type of work, ship, and occupation. One of the reasons for the variation in incidence between type of work and ship might result from differences in the voyage period in the given year. In explaining the varied incidences between occupations we hypothesize that differences in work systems and contents may be important variables to consider. It will be necessary to clarify the lifestyle and living environment of seamen to suggest appropriate measures for combating diseases prevalent in this population.