Despite increasing numbers in academic medicine, women remain underrepresented in top leadership positions. The objectives of this study were to characterize leadership positions held by department of medicine (DOM) faculty at all ranks at one Academic Health Center and to compare leadership positions held by male and female faculty. This was a cross-sectional survey to collect information on all leadership positions from 16 divisions in the DOM at the Johns Hopkins University School of Medicine in early 2012, including type of position, method used to fill the position, and financial compensation. Chi-square testing was used to compare leadership position characteristics by rank and gender. The study included 474 DOM faculty at the rank of instructor or higher; 38% were women. Of the 258 leadership positions identified, 35% were held by women. More leadership positions among assistant professors were held by women compared with men (56% of positions vs. 44%), with women assistant professors more likely to hold a leadership position than men (p=0.03). Numbers of women faculty declined at higher ranks, with leadership positions remaining proportionate to faculty representation. Most division director positions (88%) were held by men, and most leadership positions were compensated (89%) and appointed by the DOM chair or a division director (80%). Leadership positions held by women and men were proportionate to faculty representation, although the top leadership positions were held almost exclusively by men. While female assistant professors were more likely to hold leadership positions than male assistant professors, these positions appear to be low status positions and it is not clear that they contribute to professional advancement, as few women hold the rank of full professor. Effective interventions are needed to address the gender disparity in top leadership positions.