Training in scientific research methods and skills is a vital part of Dutch specialist training in intellectual disability medicine. The authors evaluated results of such training at one Dutch university medical facility that had an obligatory research program involving projects conducted by the physicians-in-training (topics, teamwork, acquired competencies, and products). Since 2000, 28 research projects were started, and 24 of them were completed by teams made up of two to five trainees. Project topics included syndrome-related comorbidity (n = 8), lifestyle (n = 2), specific medical conditions (n = 5), diagnostic methods (n = 5), and care by intellectual disability physicians (n = 8). Sixteen of the study designs were cross-section observational, five were retrospective file reviews, one dealt with instrument development, three were qualitative, and three were literature studies. Structured exit evaluation interviews with 57 trainees (20 teams) showed that teamwork was appreciated positively by 17 of the teams, negatively by one, and mixed by two teams. While skills in literature search were reported as competencies present prior to the specialist training, additional basic scientific competencies were reported as acquired or improved by over 50% of trainees (including translating clinical into research questions, literature appraisal, protocol writing, data collection in the field, data entry, critical-analytical competency, and dealing with feedback and criticism). Trainee end products include 16 written reports, three journal articles in Dutch-language publications, eight articles in international journals, and 14 international congress presentations/publications.