Studies have continuously shown that fewer women than men achieve leadership positions in academic medicine. In the current study we explored gender differences in clinical position among academic physicians at three university hospitals, each in a different European country. These countries, Sweden, the Netherlands and Austria, differ in terms of gender equality. We analyzed whether the number of children, working hours or publications could explain gender differences in physicians’ clinical position. In this cross-sectional questionnaire study 1333 (54% female) physicians participated. Physicians were asked about their gender, age, number of children, working hours and clinical position. We used structural equation models to explore the influence of gender on the physicians’ clinical position in each of the three countries. We explored whether the association between gender and clinical position could be explained by number of children, working hours or publication activity. The analyses revealed that at all three university hospitals gender influenced clinical position. These gender differences in clinical position could be partly explained by gender differences in publication activity. Female physicians as compared to male physicians were likely to publish fewer articles, and in turn these lower publication numbers were associated with lower clinical positions. The number of children or working hours did not explain gender differences in publication activity or clinical position. Therefore, factors other than unequal allocation of household labor, such as the academic working environment, may still disproportionately disadvantage women’s progress, even at universities in countries with high rates of gender equality such as Sweden.