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Background: The disruption of health and medical education by the COVID-19 pandemic made educators question the effect of online setting on students' learning, motivation, self-efficacy and preference. In light of the health care staff shortage online scalable education seemed relevant. Reviews on the effect of online medical education called for high quality RCTs, which are increasingly relevant with rapid technological development and widespread adaption of online learning in universities. The objective of this trial is to compare standardized and feasible outcomes of an online and an onsite setting of a research course regarding the efficacy for PhD students within health and medical sciences: Primarily on learning of research methodology and secondly on preference, motivation, self-efficacy on short term and academic achievements on long term. Based on the authors experience with conducting courses during the pandemic, the hypothesis is that student preferred onsite setting is different to online setting., Methods: Cluster randomized trial with two parallel groups. Two PhD research training courses at the University of Copenhagen are randomized to online (Zoom) or onsite (The Parker Institute, Denmark) setting. Enrolled students are invited to participate in the study. Primary outcome is short term learning. Secondary outcomes are short term preference, motivation, self-efficacy, and long-term academic achievements. Standardized, reproducible and feasible outcomes will be measured by tailor made multiple choice questionnaires, evaluation survey, frequently used Intrinsic Motivation Inventory, Single Item Self-Efficacy Question, and Google Scholar publication data. Sample size is calculated to 20 clusters and courses are randomized by a computer random number generator. Statistical analyses will be performed blinded by an external statistical expert., Discussion: Primary outcome and secondary significant outcomes will be compared and contrasted with relevant literature. Limitations include geographical setting; bias include lack of blinding and strengths are robust assessment methods in a well-established conceptual framework. Generalizability to PhD education in other disciplines is high. Results of this study will both have implications for students and educators involved in research training courses in health and medical education and for the patients who ultimately benefits from this training., Trial Registration: Retrospectively registered at ClinicalTrials.gov: NCT05736627. SPIRIT guidelines are followed., (© 2024. The Author(s).)