Background Fishing has always been a dangerous occupation, and numerous factors have a direct or indirect impact on the health of fisherman. Aims To examine the health, safety and working conditions of small-scale fishing fleets in the Turkish Aegean Sea coasts. Methods Data were obtained from a questionnaire distributed to a random sample of small-scale fishermen along the Aegean Sea coast. Data collection took place between September 2009 and January 2010. Results Out of 5714 Aegean Sea small-scale fishermen, 1166 from 76 fishing ports participated. Twenty-nine per cent of fishermen did not have any social security cover. The most prevalent health problems (using International Classification of Diseases and Related Health Problems 10th Revision [ICD-10]) found were musculoskeletal problems (e.g. discopathies, muscular strain, rheumatism) and eye, ear-nose, digestive and urinary system problems. Alcohol consumption was high (68%) in fishermen and 72% reported that they smoked more during fishing trips. Health problems appeared to be associated with a number of factors including migrant status, income satisfaction, rank, type of fishing and cumulative work per year. Conclusions In Turkey, small-scale fishermen experience a significant number of health problems and have unhealthy lifestyles. Interventions designed to improve working conditions of small-scale fishermen could help to reduce the number of occupational injuries, which in turn may impact positively on their health. Prevention policies to reduce alcohol and tobacco consumption should also be developed.