Background: Surprisingly little research is available to explain the well-documented organizational and societal influences on persistent inequities in advancement of women faculty. Methods: The Systems of Career Influences Model is a framework for exploring factors influencing women's progression to advanced academic rank, executive positions, and informal leadership roles in academic medicine. The model situates faculty as agents within a complex adaptive system consisting of a trajectory of career advancement with opportunities for formal professional development programming; a dynamic system of influences of organizational policies, practices, and culture; and a dynamic system of individual choices and decisions. These systems of influence may promote or inhibit career advancement. Within this system, women weigh competing influences to make career advancement decisions, and leaders of academic health centers prioritize limited resources to support the school's mission. Results and Conclusions: The Systems of Career Influences Model proved useful to identify key research questions. We used the model to probe how research in academic career development might be applied to content and methods of formal professional development programs. We generated a series of questions and hypotheses about how professional development programs might influence professional development of health science faculty members. Using the model as a guide, we developed a study using a quantitative and qualitative design. These analyses should provide insight into what works in recruiting and supporting productive men and women faculty in academic medical centers.