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Background Studies on medical repatriation of seafarers due to illnesses and injuries have been limited. The aim of the study was to describe the epidemiology of medical repatriation among Filipino seafarers. Materials and methods We performed a retrospective analysis of records from January 2010 to December 2014 of medical repatriations of Filipino seafarers from the claims and legal departments of different manning agencies in Manila, Philippines. Results We analysed data from a total of 6,759 medical repatriation cases in a 5-year period, representing 174 shipping companies and 2,256 vessels. The total number of seafarers deployed from the manning agencies where we obtained data was 388,963 with the rate of medical repatriations calculated at 1.7%. We used the 10th revision of the International Statistical Classification of Diseases and Related Health Problems (ICD-10) to determine the most common causes of repatriation. We found that these were injuries (trauma), musculoskeletal disorders, gastrointestinal problems, and genitourinary illnesses. We also conducted an analysis of the most common clinical problems per organ system. Conclusions Filipinos represent the most numerous group of seafarers in the world. Profiling their health issues may help in optimising current protocols, implementing health surveillance programs, and formulating health policies for seafaring personnel. In addition, our study results may help physicians performing pre-employment medical examinations to identify and manage conditions that are at a high risk of medical repatriation.