ObjectivesMedicine is facing a physician-scientist shortage. By offering extracurricular research programmes (ERPs), the physician-scientist training pipeline could already start in undergraduate phases of medical training. However, previous studies into the effects of ERPs are mainly retrospective and lack baseline measurements and control groups. Therefore, the current study mimics a randomised controlled trial to examine the effects of an ERP.DesignProspective cohort study with baseline measurement and comparable control group.SettingOne cohort of 315 medical undergraduates in one Dutch University Medical Center are surveyed yearly. To examine the effects of the ERP on academic achievement and motivational factors, regression analyses were used to compare ERP students to students showing ERP-interest only, adjusted for relevant baseline scores.ParticipantsOut of the 315 students of the whole cohort, 56 participated within the ERP and are thus included. These ERP students are compared with 38 students showing ERP-interest only (ie, control group).Primary outcome measureAcademic achievement after 2 years (ie, in-time bachelor completion, bachelor grade point average (GPA)) and motivational factors after 18 months (ie, intrinsic motivation for research, research self-efficacy, perceptions of research, curiosity).ResultsERP participation is related to a higher odds of obtaining a bachelor degree in the appointed amount of time (adjusted OR=2.95, 95% CI 0.83 to 10.52). Furthermore, starting the ERP resulted in higher levels of intrinsic motivation for research, also after adjusting for gender, age, first-year GPA and motivational baseline scores (β=0.33, 95% CI 0.04 to 0.63). No effect was found on research self-efficacy beliefs, perceptions of research and curiosity.ConclusionsPrevious research suggested that intrinsic motivation is related to short-term and long-term research engagement. As our findings indicate that starting the ERP is related to increased levels of intrinsic motivation for research, ERPs for undergraduates could be seen as an important first step in the physician-scientist pipeline.