BACKGROUND This cross-cultural study was designed to examine cultural differences in empathy levels of first-year medical students. METHODS A total of 257 students from the academic year 2010/11, 131 at Jimma University, Ethiopia, and 126 at the Ludwig Maximilian University, Munich, Germany, completed the Balanced Emotional Empathy Scale (BEES), the Reading the Mind in the Eyes (RME-R) test, and a questionnaire on sociodemographic and cultural characteristics. Furthermore, we conducted a qualitative analysis of the students' personal views on the definition of empathy and possible influencing factors. Group comparisons and correlation analyses of empathy scores were performed for the entire cohort and for the Jimma and Munich students separately. We used a regression tree analysis to identify factors influencing the BEES. RESULTS The male students in Jimma (39.1 ± 22.3) scored significantly higher in the BEES than those male students from Munich (27.2 ± 22.6; p = 0.0002). There was no significant difference between the female groups. We found a moderate, positive correlation between the BEES and RME-R test, i.e. between emotional and cognitive empathy, within each university. Nevertheless, the RME-R test, which shows only Caucasian eyes, appears not to be suitable for use in other cultures. CONCLUSIONS The main findings of our study were the influence of culture, religion, specialization choice, and gender on emotional empathy (assessed with the BEES) and cognitive empathy (assessed with the RME-R test) in first-year medical students. Further research is required into the nature of empathy in worldwide medical curricula.