BACKGROUND: Adolescent tobacco smoking is a major health concern in Chile. Schools may be able to influence adolescent behaviour regarding smoking; however, this topic has received limited research attention in Latin-American countries. Moreover, the prevalence of cigarette smoking varies between schools, and some of this variability may be explained by school factors. This article examines the inter-school variability in student smoking in a large sample of Chilean schools and identifies the school- and student-level characteristics associated with cigarette smoking. METHODS: This cross-sectional study used self-reported student-level data from 45,273 students from 1462 schools and official data from these schools provided by the Chilean Ministry of Education (2007). Student smoking behaviour was used as an outcome, and individual-level and school-level features were used as explanatory variables. Logistic multilevel modelling was used to analyse the data. RESULTS: The mean prevalence of smoking in the 1462 schools was 39.9 %. The null model indicated that 8 % of the variance in smoking behaviour was explained by schools; and in the final model, controlled by individual- and school-level variables, the variance explained by schools dropped to 2.4 %. The main school-level variables explaining the school influence were school bonding, school truancy and school achievement. CONCLUSIONS: This is the first study to examine the extent to which student smoking varies between Chilean schools and to identify some of the school factors associated with this inter-school variability. Although most variation in smoking prevalence lies between students within schools, there is sufficient between-school variation to be of interest to educators and policy makers.