Objectives Whether salary disparities exist between men and women in medical education leadership roles is not known. The study objective was to determine whether salary disparities exist between male and female Internal Medicine residency program directors, and if so, to identify factors associated with the disparities and explore historical trends. Methods The annual Association of Program Directors in Internal Medicine (APDIM) survey in August 2012 included items to assess the salary and demographic characteristics of program directors, which were merged with publically available program data. To assess historical trends, we used similarly obtained survey data from 2008 to 2011. The study included program directors of 370 APDIM member programs, representing 95.6% of the 387 accredited Internal Medicine training programs in the United States and Puerto Rico. Of the 370 APDIM member programs, 241 (65.1%) completed the survey, of whom 169 (70.1%) were men and 72 (29.9%) were women. Program directors' total annual salary, measured in $25,000 increments, ranged from $75,000 or less to more than $400,000. Historical trends of mode salary by gender from 2008 to 2012 were assessed. Results The mode salary was $200,000 to 225,000 for men and $175,000 to $200,000 for women (P =.0005). After controlling for academic rank, career in general internal medicine, and program director age, the distribution of salary remained different by gender (P =.004). Historical trends show that the difference in mode salary has persisted since 2008. Conclusions Leaders in academic medical centers, residency and fellowship directors, and all faculty in medical education need to be aware that salary disparities cited decades ago persist in this sample of medical educators. Closing the gender gap will require continued advocacy for measuring and reporting salary gaps, and changing the culture of academic medical centers.