Women are under-represented in academic medicine. We reviewed the empirical evidence focusing on the reasons for women's choice or rejection of careers in academic medicine. Using a systematic search, we identified 52 studies published between 1985, and 2015. More than half had methodological limitations and most were from North America. Eight main themes were explored in these studies. There was consistent evidence for four of these themes: women are interested in teaching more than in research; participation in research can encourage women into academic medicine; women lack adequate mentors and role models; and women experience gender discrimination and bias. The evidence was conflicting on four themes: women are less interested in research than men; women lose commitment to research as their education and training progress; women are deterred from academic careers by financial considerations; and women are deterred by concerns about work–life balance. Inconsistency of findings across studies suggests significant opportunities to overcome barriers by providing a more enabling environment. We identified substantial gaps in the scientific literature that could form the focus of future research, including shifting the focus from individuals' career choices to the societal and organisational contexts and cultures within which those choices are made; extending the evidence base to include a wider range of countries and settings; and testing the efficacy of interventions.