A 17-year longitudinal follow-up of the National Faculty Survey was conducted with a random sample of faculty from 24 US medical schools. The study assessed the longitudinal patterns by gender in compensation, and to understand factors associated with these differences in a longitudinal cohort. Findings indicate that institutional actions to address these disparities should include both initial appointment and annual salary equity reviews, training of senior faculty and administrators to understand implicit bias, and training of women faculty in negotiating skills.