To investigate changes in Japanese physician workforce participation over time, with a focus on gender differences in career patterns.Subjects were Japanese physicians who had participated in the biennial national physician survey at least once between 1980 and 2002. Two cohorts of physicians were traced: those who were between 25 and 64 years old and were already on the physician registry as of 1980 (Cohort 1980), and those on the registry as of 1990 (Cohort 1990). Workforce participation rates, as measured by the proportion of physicians working in the field of health care, were calculated for every other year until 2002. Then, 10-year averages for workforce participation rates were calculated and compared by cohort and gender.In both cohorts, the workforce participation rates of female physicians revealed a marked decline in their late 20s and 30s; in contrast, those of male physicians remained at a high level until the age of 65. The average workforce participation rate of female physicians was significantly lower than that of male physicians, both in Cohort 1980 and Cohort 1990, and both male and female physicians in Cohort 1990 had a significantly lower average than physicians in Cohort 1980.Effective measures should be taken to help physicians continue to work, and especially, to alleviate the decline in workforce participation among young female physicians.