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The aim of this study was to assess psychological morbidity and symptoms of burnout in medical students during their undergraduate training, and to identify baseline factors that predict psychological morbidity in students in the final year of the course. It was a 5-year prospective longitudinal cohort study. Students were assessed in years 1, 4 and 5 of their medical undergraduate training by means of the GHQ-12 and the Maslach Burnout Inventory. 172 (84.3%), 157 (77.0%) and 155 (75.9%) students out of an original group of 204 completed assessments in years 1, 4 and 5, respectively. 18 students were above threshold on the GHQ-12 on all three occasions, 25 on two occasions and 43 on one occasion; 69 students were never a 'case'. Students who were cases on two or more occasions were more likely to find the medical course stressful during the first year, but not subsequent years. There was no significant difference between the percentages of men and women who scored as cases on the GHQ-12 in any of the years. The best predictor of psychological morbidity in the final year of the course was the GHQ-12 score in year 1. This study suggests that a small group of students repeatedly experience psychological distress during their medical training.