The shortage of physicians has become a serious problem in Japan. It has been pointed out that an increase in the number of female doctors may contribute to the aggravation of this shortage because it is known that women work fewer hours than male doctors. Here, we investigated how many female doctors had ever resigned from a full-time position, and elucidated the reasons why female doctors find it difficult to stay in full-time employment. An alumnae survey of 2 private medical schools was conducted in 2007. A self-administered questionnaire was sent to 1423 graduates and 711 responded with informed consent (response rate, 50%; mean age, 39 years). Overall, 55% of the respondents had previously resigned from full-time employment, of which 90% resigned within 10 years of graduating from medical school. The difficulty in balancing work, childbirth and child rearing (45%) were the top 2 reasons for resignation, followed by physical problems (12%) and long working hours (8%). Among those who resigned, only 33% returned to full-time employment. Women who had at least 1 child were only 30% of those who had never resigned and 84% of those who had previously resigned. The majority of study subjects, regardless of experience of resignation (88%), agreed that women should continue to work even after childbirth. In conclusion, the results of this study suggested that many female doctors resigned from a full-time position within 10 years of graduating from medical school, largely because of the gender role stereotype and poor working conditions.