The medical fitness of pilots is part of the civil aviation safety scenery. This study aimed to analyze the health problems occurring among Korean commercial pilots. Three data sources were used to identify the health problems: 7,574 aviation medical examination data, 5,400 sick leaves and 39 cases of a decrease in medical fitness during flight duty period and layover of Korean commercial pilots who have been working for K airline from Jan. 1, 2016 to Dec. 31, 2018. This study was retrospectively analyzed using SPSS 22 statistical program. Waiver of medical certificates was an average 11.9% of total issuance for 3 years, with a denial of 0.1%. The leading cause of denial of medical certificates was predominantly of cardiovascular cause (55.6%). Mild respiratory and digestive disease accounted for 82% of total sick prevalence and 68% of total sick days. The psychiatric and cardiovascular disease were ranked high according to the number of days lost per case. The most common cause of decrease in medical fitness during flight duty period was acute abdominal pain (36.4%) and musculoskeletal disorder (40%) when staying abroad. Aeromedical emphasis on minimizing cardiovascular risk remains appropriate. Major pilot health problems identified in this study should be considered in establishing pilot health promotion programs for aviation safety.