A growing number of physicians are leaving their hospitals because of painful working conditions in hospitals throughout Japan. We set out to analyze the interrelationships between working conditions, job satisfaction, burnout and mental health among Japanese physicians. A cross-sectional survey was conducted in 2007 for hospital physicians throughout Japan. A path analysis based on structural equation modeling was utilized for examining the interrelationships between work control, on-call duty volume, job satisfaction (the Japan Hospital Physicians Satisfaction Scale), burnout (the Japanese version of the Maslach Burnout Inventory) and mental health (the General Health Questionnaire). Of 336 physicians who received a solicitation E-mail, 236 participated in our study (response rate, 70%). Sixty physicians (25.4%) were women with a mean age of 41 yr. In the path analysis, burnout and poor mental health were related directly to job dissatisfaction and short sleeping time, while they were related indirectly to poor work control and heavy on-call duty. In the multi-group path analysis of both genders, sleeping time was related to job satisfaction more likely among female physicians but less among male physicians. Healthcare policy makers need to implement immediate, extensive and decisive measures to improve work condition and to reduce overwork among hospital physicians.