Several studies explored gender inequalities in research, but only limited data are available concerning general internal medicine and family medicine. We aimed to assess the level of gender inequalities in Swiss academic medical research. In this bibliometric study conducted in March 2020, we selected all senior hospital physicians practicing internal medicine or family medicine in the six Swiss university hospitals. The list of these physicians was extracted from the hospitals' websites. We recorded their socio-demographic characteristics. Then, using Web of Science, we retrieved the number of publications (overall, as first author, per year, per year as first author), the proportion of publications as first author, the number of citations (overall, per year, per publication) and the h-index, and we compared the data by gender. 367 senior physicians were included in the study [female physicians: 172 (47%), internal medicine: 187 (51%)]. Female physicians were four times less likely to be a professor (5% vs. 20%, p value < 0.001) and half as often heads of division or staff physicians (19% vs. 40%, p value < 0.001). The proportion of physicians having published at least one article was lower among women than men (79% vs. 90%, p value 0.003). Finally, all bibliometric indices were associated with male gender (incident rate ratios ranging from 1.9 [(95% CI 1.3–2.8), p value 0.001] for number of citations per publication to 9.3 [(95% CI 5.3–16.2), p value < 0.001] for number of citations), except the proportion of publications as first author that was associated with female gender [odds ratio 1.7 (95% CI 1.2–2.3), p value 0.003). Our data suggest a “leaky pipeline” phenomenon (a lower proportion of women moving up the academic ladder). In addition, with the exception of the proportion of publications as first author, all bibliometric indices were lower for female than male physicians.