MD–PhD training takes, on average, 8 years to complete and involves two transitions, an MD-preclinical to PhD-research phase and a PhD-research to MD-clinical phase. There is a paucity of research about MD–PhD students’ experiences during each transition. This study examined transition experiences reported by 48 MD–PhD students who had experienced at least one of these transitions during their training. We purposefully sampled medical schools across the United States to recruit participants. Semistructured interviews were audio-recorded and transcribed for analysis; items focused on academic and social experiences within and outside their programs. Using a phenomenological approach and analytic induction, we examined students’ transition experiences during their MD–PhD programs. Five broad themes emerged centering on multiple needs: mentoring, facilitating integration with students in each phase, integrating the curriculum to foster mastery of skills needed for each phase, awareness of cultural differences between MD and PhD training, and support. None of the respondents attributed their transition experiences to gender or race/ethnicity. Students emphasized the need for mentoring by MD–PhD faculty and better institutional and program supports to mitigate feelings of isolation and help students relearn knowledge for clinical clerkships and ease re-entry into the hospital culture, which differs substantially from the research culture.