BackgroundPoor mental health among medical students is widely acknowledged. Studies on mental health among medical students of Nepal are lacking. Therefore, we conducted a study to determine the prevalence of mental disorders.MethodsA cross-sectional study was conducted among medical students at KIST Medical College and Teaching Hospital, Nepal from December 2016 to February 2017. Our survey instrument consisted of the Patient Health Questionnaire (PHQ) and questions about socio-demographic factors, smoking, marijuana use, suicidal ideation and thoughts of dropping out of medical school.ResultsThe prevalence rates were 29.2% (95% CI, 24.4% – 34.3%) depression, 22.4% (95% CI, 18.0% – 26.9%) medium to highly severe somatic symptoms, 4.1% (95% CI, 2.0% – 6.2%) panic syndrome, 5.8% (95% CI, 3.4% – 8.3%) other anxiety syndrome, 5% (95% CI, 2.7% – 7.3%) binge eating disorder and 1.2% (95% CI, 0.0% - 2.3%) bulimia nervosa. Sixteen students [4.7% (95% CI, 2.4% – 6.9%)] seriously considered committing suicide while in medical school. Thirty-four students [9.9% (95% CI, 6.8% – 13.1%)] considered dropping out of medical school within the past month. About 15% (95% CI, 11.1% – 18.6%) of the students reported use of marijuana during medical school.ConclusionsWe found high prevalence of poor mental health among medical students of Nepal. Future studies are required to identify the factors associated with poor mental health.Electronic supplementary materialThe online version of this article (10.1186/s12909-017-1083-0) contains supplementary material, which is available to authorized users.