BackgroundFaculty departure can present significant intellectual costs to an institution. The authors sought to identify the reasons for clinical and non-clinical faculty departures at one academic medical center (AMC).MethodIn May and June 2010, the authors surveyed 137 faculty members who left a west coast School of Medicine (SOM) between 1999 and 2009. In May and June 2015, the same survey was sent to 40 faculty members who left the SOM between 2010-2014, for a total sample size of 177 former faculty members. The survey probed work history and experience, reasons for departure, and satisfaction at the SOM versus their current workplace. Statistical analyses included Pearson’s chi-square test of independence and independent sample t-tests to understand quantitative differences between clinical and non-clinical respondents, as well as coding of qualitative open-ended responses.ResultsEighty-eight faculty members responded (50%), including three who had since returned to the SOM. Overall, professional and advancement opportunities, salary concerns, and personal/family reasons were the three most cited factors for leaving. The average length of time at this SOM was shorter for faculty in clinical roles, who expressed lower workplace satisfaction and were more likely to perceive incongruence and inaccuracy in institutional expectations for their success than those in non-clinical roles. Clinical faculty respondents noted difficulty in balancing competing demands and navigating institutional expectations for advancement as reasons for leaving.ConclusionsAMCs may not be meeting faculty needs, especially those in clinical roles who balance multiple missions as clinicians, researchers, and educators. Institutions should address the challenges these faculty face in order to best recruit, retain, and advance faculty.Electronic supplementary materialThe online version of this article (doi:10.1186/s12909-016-0830-y) contains supplementary material, which is available to authorized users.