Background@#In South Korea, the legal maximum working hours per week for medical residents is 88 hours, which are longer than those for other occupations, and the intensity of the workload is also remarkably high. Long working hours and job-related stress can worsen the health status of residents. This study aimed to analyze the four-year annual health checkup (AHC) data of residents to identify changes in their health indicators. @*Methods@#This study included 457 male residents who received 4 years of training at a university hospital. They underwent an AHC every year during the training period. Changes in health indicators and related factors over the 4 years were investigated. @*Results@#Body mass indices (BMI), blood pressures (BPs), liver function test (LFT) results, and total cholesterol (TC) levels were significantly worsened during the training period.The increases were the highest in the early training years, between the 2 nd and 1 st AHC.The working hours of the fourth-year residents were the shortest and showed low smoking and drinking rates and high regular exercise rates. On comparing by department, surgical residents showed the highest increases in BMI, diastolic BP, and fasting blood glucose (FBG), LFT enzyme, and TC levels during the training period, compared to residents from the medical and clinical support departments. Residents who were working ≥ 80 hours showed significantly higher FBG and LFT enzyme levels than those working < 80 hours. @*Conclusion@#This study is meaningful as it is the first study in Korea to investigate the changes in the health of residents through objective health indicators. The possibility of the 4-year training period adversely affecting the health of residents was confirmed. Health indicators were significantly worsened, especially in the early training period, in surgical residents, and in residents who worked for long hours. Efforts are needed to restrict long working hours and distribute workload during the 4-year training period.