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Purpose To conduct a randomized controlled trial (RCT) to evaluate the effects of different mentoring interventions on the basic psychological need satisfaction of underrepresented minorities and women in academia. Method Participants were 150 mentor/protégé dyads from three academic medical centers and eight other colleges and universities in western and central New York, randomized from 2010–2013 into: mentor training (using principles of self-determination theory); peer mentoring for protégés; mentor training and peer mentoring for protégés combined; or control/usual practice. Protégé participants were graduate students, fellows and junior faculty who were from underrepresented groups based on race, ethnicity, gender, or disability. The primary analysis was a comparison of intervention effects on changes in protégés’ satisfaction of their basic psychological needs (competence, autonomy and relatedness) with their mentor. They completed a well-validated, online questionnaire every 2 months for 1 year. Results There was no significant effect at the end of 1 year of either mentor training or peer mentoring on protégés’ psychological basic need satisfaction with mentor specifically or at work in general. Exploratory analyses showed a significant effect of the mentor-based intervention on the protégés’ overall psychological need satisfaction with their mentor at 2 months, the time point closest to completing mentor training. Conclusions This RCT showed a potential short-term effect of mentor training on changing basic psychological need satisfaction of underrepresented scholars with their mentors. Despite the lack of sustained effect of either mentor training or peer mentoring, these short-term changes suggest feasibility and potential for future study.