Background Previous researches suggested that minority students are more exposed to discrimination and mistreatment at university, therefore may have higher risk of mental and physical health problems. Methods An online questionnaire was conducted among medical students of the 4 Hungarian medical universities (N=530). The survey contained questions about general demographic data, health behavior, burnout, mental and physical health issues and discrimination. Results 29.6% of students self-identified as minority. High level burnout was indicated by 48.1% of respondents, while another 27.0% showed moderate level. High level burn-out was associated with minority status (84.6% vs. 71.0%; p<0.001), discrimination (83.0% vs. 68.5%, p< 0.001), lower level of social support (89.0% vs 69.0%, p<0.001) and higher levels of perceived stress (57.1% vs. 95.4%) in the chi-squared test. Higher scores on trait (B = 0.123; p<0.001) and state anxiety (B = 0.082; p<0.001) subscales of STAI and lower score of resilience (B= -0.168; p<0.001) were significantly associated with higher level of burnout in the univariate model. In our final analysis, perceived stress, resilience, minority identity and experienced discrimination remained significant. Conclusions Belonging to a minority community might need to be considered an essential factor leading to burnout in Hungarian medical students. Our research suggests that minority medical students have poorer mental health and higher risk for burnout.