Abstract Background Aiming at generating evidence for formulating targeted and cost-effective public health interventions for the effective control of alcohol use (AU) in emerging adults in South Eastern Europe. The study’s objective was to assess if alcohol users experience adverse childhood experiences (ACE) more often than non-users, and to identify which ACE victims are the most vulnerable to AU. Methods The data was collected in 2010–2012 in two cross-sectional studies conducted in university settings in Montenegro and Romania (overall response rate 89.1%). In the present study, 3,283 students were included. The international ACE Study Questionnaires were used as a base for study instruments for collecting information on ACEs, health behaviours, and socio-economic factors. The association between AU and individual ACEs, adjusted to background factors, was assessed by using logistic regression. Results From the child maltreatment group, three ACEs were included in the final model as statistically significantly associated with AU, all of them from physical neglect/abuse types: frequently being hit so hard to have marks or being injured (OR=1.68; p=0.012), frequently being spanked (OR=1.38; p=0.012), and frequently having no person to take to the doctor if necessary (OR=0.58; p=0.031). From the household dysfunction group, two ACEs were included in the final model: exposure to mental health problems in the household (OR=2.85; p<0.001), and living with a problematic drinker/alcoholic (OR=1.51; p=0.019). Conclusions The effect of exposure to ACEs on AU persists into emerging adulthood. This should be considered when developing cost-effective response to AU burden through targeted interventions, in particular in settings with scarce resources.