Self-harm has become a nonspecific symptom of mental distress that is most prevalent in the adolescent population. Since it is often a hidden problem, it is important to focus on preventing it. This study used the data from the Croatian leg of the European School Survey Project on Alcohol and Other Drugs to assess certain risk factors and possible protective factors for self-harm thoughts among 16-year-olds in Croatia. Using binary logistic regression, we identified that being female, having less family support and less parental knowledge of adolescents' activities, more frequent cannabis use, more compulsive Internet use and more frequent depressive symptoms significantly increased the likelihood of self-harm thoughts in this sample. Identifying factors that lead to thoughts of self-harm may open a potential space for self-harm prevention before those thoughts progress into behavior.