Introduction: The paucity and maldistribution of physicians among various specialties are key issues facing the Japanese health care system. Studies have shown that young physicians place more emphasis on work-life balance while selecting their specialty and that they prefer controllable lifestyle (CL) specialties over noncontrollable lifestyle (NCL) specialties. As this may be a cause of maldistribution, we investigated the relationship between views on work-life balance and specialty selection among young physicians in Japan.Methods: An online questionnaire was sent to 1451 residents (postgraduate years 1-5) at 60 Japanese Red Cross hospitals across Japan. Results: In all, 226 physicians responded (response rate: 15%), with 21% in CL and 74% in NCL specialties. When compared with NCL specialties, CL specialties had less overtime (43% vs. 16%, p = 0.001), considered life to be more important than work (26% vs. 15%, p = 0.018), and were more likely to give precedence to work-life balance over medical interest while choosing their specialty (49% vs. 30%, p < 0.001). Furthermore, physicians were more likely to change their choice of specialty, contrary to their professional interest, because of social reasons (49% vs. 26%, p = 0.007). Conclusions: Our study suggests that young physicians in CL specialties have better working hours and place more emphasis on work-life balance while choosing their specialty compared with those in NCL specialties. The increase in the number of physicians in CL specialties is likely attributable to the growing preference for an optimal work-life balance among young physicians; this seems to have increased the maldistribution of physicians among various specialties. Institutional mechanisms to support the lifestyle of physicians (especially in NCL specialties) are required to provide a balanced medical service in Japan.