Background: University studying is demanding on the mental as well as the physical side of the students. However, studying medicine is even more challenging – the study is six years long, and it is tough to remember more information. The study changed the social life of students, and the students didn't have enough time to relax. The examinations of students are full of stress. Stress harms health, especially in the gastrointestinal tract (autonomic nervous system). Aims: The first study evaluated eating habits during and outside an examination period and the effect on the health of medical students in Slovakia. Methods: We made the questionnaire and distributed it online to medical students at the Faculty of Medicine in Bratislava, Slovakia. A total of 587 students from the 1st to 6th year completed self-report measures of BMI, academic stress, eating habits and the occurrence or development of digestive problems during the study. Results: Our results showed that most respondents were of average range weight and ate a well-balanced diet (90%); more than half of the participants had breakfast regularly, and almost half of the students ate junk food a few times per week. Our participants consumed less food but more junk food and energy drinks during the exam period, which can cause obesity and digestive problems. Conclusion: Our findings confirm that subjective academic feelings of stress play an important role in eating habit changes and in the origin of digestive disorders in our medical students.