Abstract Background Research is of great value to make advancements within the medical field and, ultimately, offer the best possible patient care. Physician-scientists are key in contributing to the development of medicine, as they can bridge the gap between research and practice. However, medicine currently faces a physician-scientist shortage. A possible solution to cultivate physician-scientists is to engage medical students in research in early phases of medical school. Evidence-based strategies to stimulate positive perceptions of and motivation for research among students could help to enhance research engagement. Consequently, understanding of students’ perceptions of and motivation for research is needed. Therefore, this study aimed to identify conditions under which students develop positive perceptions of and motivation for research by answering the following sub-questions: 1) how do first-year medical students perceive research? and 2) which factors contribute to motivation or demotivation for conducting research? Methods We conducted a qualitative study with individual interviews using a grounded theory approach, involving 13 purposively sampled first-year medical students at Leiden University Medical Center. Results Our results suggest that first-year students are already able to identify many aspects of research. Students elaborated on the relevance of research for professional practice and personal development. Furthermore, our results suggest a relationship between perceptions of and motivation for research. Some perceptions were identical to motivating or demotivating factors to conduct research, like the relevance of research for practice and performing statistics respectively. Other motivating factors were, among others, acknowledgment, autonomy, and inspiring role models. Demotivating factors were, among others, lack of autonomy and relevance, and inadequate collaboration. Conclusions Our results contribute to the idea that perceptions of research are related to motivation for research, which offers possibilities for interventions to promote motivation for research by making use of student perceptions of research. Consequently, practical implications to stimulate research engagement in early phases of medical school are provided. Moreover, the results contribute to existing motivational theories like Theory of Planned Behavior and Self-Determination Theory within this specific domain.