Abstract Background Adolescence is a period of psychological development which is associated with an increased risk of developing mental health disorders. Medical students have a higher prevalence of depression compared to the general population, but they are given low priority in the healthcare system. The aim of this study was to examine the prevalence of clinically significant scores on the Patient Health Questionnaire 9 (PHQ-9), and factors associated with clinically significant scores. Methods The research was conducted through a cross-sectional study among fifth-year medical students, using a 95-item questionnaire anonymously filled out. The questionnaire examined: socio-demographic and socio-economic characteristics of the students; students’ lifestyles (including alcohol consumption, binge drinking, smoking cigarettes, electronic cigarettes, use any of other tobacco products); Patient Health Questionnaire (PHQ-9); International Physical Activity Questionnaire (IPAQ); Zung’s Anxiety Scale; and Problematic Internet Use Scale. Based on the score on PHQ-9, the participants were classified in two groups: with clinically significant scores (score ≥10) and without clinically significant scores (score <10). Results The study included 461 medical students who completed the PHQ-9. Average score on PHQ-9 scale was 5.25±4.53 and total of 66 students (14.3%) had the PHQ-9 indicative of clinically significant depressive symptoms (PHQ-9 ≥10). The clinically significant depression was associated with smoking of any tobacco product (OR:3.02, 95% CI: 1.37-6.63), score on social support scale (0.94, 95% CI: 0.90-0.98), age (OR: 1.42, 95% CI: 1.06-1.90) and score on Zung anxiety scale (OR: 1.15, 95% CI: 1.16-1.34). Conclusions Considering that medical students, are at higher risk of developing clinically significant symptoms of depression, it is crucial to form psychological and social support programs. Key messages • Monitoring the mental health of young individuals holds significant importance. • It is crucial to detect risk factors in time and develop prevention programs.