The National Institute of General Medical Sciences Medical Scientist Training Program (MSTP) has been successful in producing clinician-scientists, with a majority of graduates pursuing research-related careers. However, there are a number of areas of continuing concern for the program. In particular, women and individuals from certain racial and ethnic backgrounds remain persistently underrepresented in MSTPs relative to the average college-aged U.S. population and to students receiving life sciences bachelor’s degrees. The authors, who include leaders of NIGMS, identify a number of challenges and opportunities for enhancing diversity, equity and inclusion in the MSTPs and suggest strategies for addressing them.