Background: Clinical empathy has been associated with positive outcomes for both physicians and patients such as: more accurate diagnosis and treatment, increased patient satisfaction and compliance, and lower levels of burnout and stress among physicians. International studies show mixed results regarding the development of empathy among future physicians associating medical education with decline, stability or increase in empathy levels. These mixed results are due to several study limitations. In Denmark, no investigation of Danish medical students' empathy trajectory has yet been conducted wherefore such a study is needed that optimizes the study design of earlier studies. Methods: The aim of the study is to examine and analyze empathy levels and empathy changes among Danish medical students from the four medical faculties in Denmark, employing a cross-sectional and longitudinal mixed-methods design including a control group of non-medical students. By supplementing cross-sectional and longitudinal questionnaire studies with a focus group interview study it is the aim to identify and analyze factors (including educational) that are perceived by medical students to influence the development of empathy and its expression in clinical care. Discussion: The results of the study will provide insight into the trajectory of medical students' empathy and in undergraduate and graduate students' experiences with and perceptions of empathy development. In addition, the study will provide evidence to support further research on how targeted educational programmes can best be designed to educate empathic and patient-centered physicians.