OBJECTIVE Medical education and training can directly contribute to the development of psychological distress in medical students. This can lead to catastrophic consequences such as impaired academic performance, impaired competency, medical errors and attrition from medical school. This study aimed to assess the prevalence of psychological morbidity among Iranian medical students. METHODS This was a cross-sectional study. Samples of medical students in different levels of training (basic science, clinical clerkship, internship, and residency stage) were entered into the study. The 12-item General Health Questionnaire (GHQ-12) was used to measure psychological morbidity. Both univariate and multivariate analyses were used to report on findings. RESULTS In all, 220 medical students were invited to take part in the study. Of these, 192 students agreed to fill in the questionnaire. The mean age of respondents was 25.4 (SD = 5.2) and 53% were female. Overall 49.5% of the students scored above the threshold on the GHQ-12 (score > 3.5). The results obtained from logistic regression analysis indicated that female gender and level of training were the most significant contributing factors to increased psychological distress [OR for female gender = 2.99; OR for the basic science group = 6.73]. CONCLUSIONS Psychological distress appears to be common in medical students and significantly varies by gender and level of training. The psychological well-being of medical students needs to be more carefully addressed, and closer attention to eliminating the risk factors is critical to prevent consequent adverse outcomes.