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Prior studies have found that women in academic medicine do not advance or remain in their careers in parity with men. The authors examined a cohort of faculty from the 1995 National Faculty Survey to identify predictors of advancement, retention, and leadership for women faculty.The authors followed 1,273 faculty at 24 medical schools in the continental United States for 17 years to identify predictors of advancement, retention, and leadership for women faculty. Schools were balanced for public or private status and the four Association of American Medical Colleges geographic regions. The authors used regression models to adjust for covariates: seniority, department, academic setting, and race/ethnicity.After adjusting for significant covariates, women were less likely than men to achieve the rank of professor (OR = 0.57; 95% CI, 0.43–0.78) or to remain in academic careers (OR = 0.68; 95% CI, 0.49–0.94). When number of refereed publications was added to the model, differences by gender in retention and attainment of senior rank were no longer significant. Male faculty were more likely to hold senior leadership positions after adjusting for publications (OR = 0.49; 95% CI, 0.35–0.69).Gender disparities in rank, retention, and leadership remain across the career trajectories of the faculty cohort in this study. Women were less likely to attain senior-level positions than men, even after adjusting for publication-related productivity. Institutions must examine the climate for women to ensure their academic capital is fully utilized and equal opportunity exists for leadership.