BACKGROUND The Czech Unplugged Study, inspired by the European Drug Addiction Prevention Trial, is a prospective, school-based, randomized controlled prevention trial designed to reduce the risk of alcohol, tobacco, inhalant, and illegal drug use in 6th graders in the Czech Republic. The intervention uses the comprehensive social influence model to affect alcohol and drug using norms among primary school students. METHODS Descriptive statistics and chi-square analyses were used to assess differences between the experimental and control groups on demographic characteristics and study outcomes. Multilevel techniques were used to take the hierarchical structure of the data into account. Prevalence odds ratios using the Bonferroni correction were calculated to assess the differences between the experimental (N = 914) and control (N = 839) groups on each outcome 1, 3, 12, 15, and 24 months after the end of the intervention. RESULTS Multilevel analysis using the Bonferroni correction showed statistically significant intervention effects at the final follow-up for any smoking (OR = 0.75, 99.2% CI 0.65-0.87), daily smoking (OR = 0.62, 99.2% CI 0.48-0.79), heavy smoking (OR = 0.48, 99.2% CI 0.28-0.81), any cannabis use (OR = 0.57 99.2% CI 0.42-0.77), frequent cannabis use (OR = 0.57, 99.2% CI 0.36-0.89), and any drug use (OR = 0.78, 99.2% CI 0.65-0.94). CONCLUSIONS This study adds new evidence on the effectiveness of the Unplugged school-based prevention program for primary school students in the Czech Republic.