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Abstract Background In Japan, some residents develop mental health problems. In previous studies, it was reported that long working hours might be a cause of stress reaction such as depression. There were some reports that compared residents with 80 or more working hours with those with less than 80 working hours. However, many residents are practically detained for extra-long time, designated as 100 h or more per week, for medical practice, training, self-study, etc. There have been few reports on extra-long hours of work. This study evaluated the working environment and the amount of stress experienced by first-year residents, and examined the relationship between long working hours and depression, especially in the group of extra-long working hours. Methods The study included 1241 first-year residents employed at 250 training hospitals in 2011. A self-report questionnaire was administered at the beginning of the residency and 3 months later to collect data on demographics, depressive symptoms, and training conditions (e.g., duration of work, sleep, disposable time, and night shift). Depressive symptoms were rated using the Center for Epidemiologic Studies Depression Scale. Results The mean duration of work per week was 79.4 h, with 97 residents (7.8%) working 100 h or more. At 3 months, clinically significant depressive symptoms were reported by 45.5% of residents working 100 or more h per week, which proportion was significantly greater than that for respondents working less than 60 h (P |