A lack of physician scientists as well as a high female dropout rate from academic medicine and basic life sciences is a concern in many countries. The current study analyzes academic career intentions within a sample of recent doctoral graduates from medicine and basic life sciences (N = 1109), focusing on research self-efficacy beliefs as explanatory variable of gender and disciplinary differences. To ensure that differences in research self-efficacy could not be attributed solely to objective scientific performance, we controlled for number of publications and dissertation grade. The results of multivariate analyses pointed to a strong and significant association between research self-efficacy and academic career intentions (ß = 0.49, p<0.001). The lower academic career intentions of medical doctoral graduates were no longer significant when controlling for research self-efficacy. Within the field of medicine, female doctoral graduates expressed lower research self-efficacy beliefs and academic career intentions. When controlling for research self-efficacy, the correlation between gender and academic career intention was no longer significant. In contrast, no gender differences were found within the basic life sciences with respect to neither academic career intentions nor research self-efficacy.