Weight and quality of medical doctoral theses have been discussed in Germany for years. Doctoral study programs in various graduate schools offer opportunities to improve quality of medical doctoral theses. The purpose of this study was to demonstrate distinctions and differences concerning motivation, choice of subject and the dissertation process between doctoral candidates completing the doctoral seminar for doctoral students in the Ludwig-Maximilians-University (LMU) Munich and doctoral candidates doing their doctorate individually.All 4000 medical students of the LMU obtained an online-questionnaire which was completed by 767 students (19 % response rate). The theoretical framework of this study was based upon the Self-Determination-Theory by Deci and Ryan.Doctoral candidates completing the doctoral study program were more intrinsically motivated than doctoral candidates doing their doctorate individually; no difference was found in their extrinsic motivation. In regard to choice of subject and dissertation process the doctoral students in the seminar were distinguished from the individual group by having chosen a more challenging project. They anticipated a demanding dissertation process including conference participation, publishing of papers, etc. Intrinsic motivation correlates positively with choosing a challenging project and a demanding dissertation process.High intrinsic motivation seems to be very important for autonomous scholarly practice. Our results suggest that doctoral study programs have a positive impact on intrinsic motivation and interest in research.