Objective: To assess the mental health status and associated factors of Peruvian medical students during the COVID-19 pandemic. Methods: Descriptive, multicentre, correlational study that used the “Patient Health Questionnaire-9 (PHQ-9)”, the “Generalized Anxiety Disorder-7 (GAD-7)” and the “Impact of Event Scale-Revised (IES-R)” questionnaires to evaluate mental health problems. Results: A total of 1,238 students from 8 Peruvian medical schools participated in the study. Of these, 68.5% were women, and the mean age was 21.4 years. Depressive symptoms were found in 74% of the participants, anxiety symptoms in 57% and distress symptoms in 65%. The variables associated with the development of symptoms of moderate-severe depression, anxiety and distress were: not having family economic stability, being in the first years of medical training, being female, and fearing that their medical training would be delayed and impaired. Conclusions: In a sample of medical students surveyed during the COVID-19 pandemic, mental health problems were common. The factors associated with mental health reported in this study could be useful in identifying vulnerable medical students who require timely psychosocial support and/or psychiatric care.