Background: Medical training can be a period of significant psychological distress but adequate data examining the prevalence and association of poor mental health in medical students in Nepal is lacking. This study aimed to investigate the prevalence and associated factors of depression, anxiety and stress among undergraduate medical students in Nepal. Methods: A multi-centre cross-sectional study was conducted using the Depression, Anxiety and Stress Scale (DASS-21) in addition to questions about socio-demographic characteristics of the participants. Multiple logistic regression analysis was performed to examine correlation. Results: Among the 551 participants, the prevalence of depression, anxiety and stress was 50.1%, 62.8% and 42.3% respectively. Female gender, being bullied, and dissatisfaction with one’s academic performance were significant predictors of all three outcomes. Alcohol consumption was an additional predictor of stress.. Conclusions: Nepalese medical students experience high levels of psychological distress. There is a need for relevant authorities to implement changes to the medical education system in Nepal and develop adequate support services for this population.