The socioeconomic inequality in pupils' risk behaviors has been the topic of many studies with quite contradictory findings. Furthermore, the role of socioeconomic environment has been analyzed much less often than the role of individual socioeconomic status (SES). This study examined the association between school/area-level socioeconomic environment and Croatian pupils' risk behaviors (tobacco use, drunkenness, cannabis use, early sexual initiation and fighting). Data from the WHO-Collaborative ‘Health Behavior in School-aged Children' study conducted in Croatia in 2006 (1601 secondary schools' pupils, aged 15) and census data were used. Multilevel logistic regression analyses, adjusted by gender, were performed. The individual level of SES explained the majority of differences in all risk behaviors among adolescents. Differences in tobacco use, early sexual initiation and fighting were more closely attributed to school level than area level, which was more closely associated with differences in adolescent drunkenness and cannabis use. At the individual level, high individual SES was associated with higher probability for tobacco use and drunkenness compared to low individual SES. Furthermore, school heterogeneity (compared to school homogeneity) and medium school-level SES (compared to low school-level SES) were associated with higher probability for cannabis use. Compared to the most advanced schools (gymnasiums), attending the least advanced schools (industrial and crafts schools) was associated with higher probability for fighting. Compared to low area-level SES, medium area-level SES was associated with higher probability for cannabis use and fighting. Conclusively, it was found that low SES at individual, school and area levels, school homogeneity and advanced school attendance play a protective role against risk behaviors. To reduce inequalities in pupils' risk behaviors, there is a need for community and school-based programs that take into consideration not only individual SES but also school- and area-level socioeconomic circumstances.