BACKGROUND: Adolescent smoking is still highly prevalent in Denmark. One in four 13-year olds indicates that they have tried to smoke, and one in four 15-year olds answer that they smoke regularly. Smoking is more prevalent in socioeconomically disadvantaged populations in Denmark as well as in most Western countries. Previous school-based programs to prevent smoking have shown contrasting results internationally. In Denmark, previous programs have shown limited or no effect. This indicates a need for developing a well-designed, comprehensive, and multi-component intervention aimed at Danish schools with careful implementation and thorough evaluation.This paper describes X:IT, a study including 1) the development of a 3-year school-based multi-component intervention and 2) the randomized trial investigating the effect of the intervention. The study aims at reducing the prevalence of smoking among 13 to 15-year olds by 25%. METHODS/DESIGN: The X:IT study is based on the Theory of Triadic Influences. The theory organizes factors influencing adolescent smoking into three streams: cultural environment, social situation, and personal factors. We added a fourth stream, the community aspects. The X:IT program comprises three main components: 1) smoke-free school premises, 2) parental involvement including smoke-free dialogues and smoke-free contracts between students and parents, and 3) a curricular component. The study encompasses process- and effect-evaluations as well as health economic analyses. Ninety-four schools in 17 municipalities were randomly allocated to the intervention (51 schools) or control (43 schools) group. At baseline in September 2010, 4,468 year 7 students were eligible of which 4,167 answered the baseline questionnaire (response rate = 93.3%). DISCUSSION: The X:IT study is a large, randomized controlled trial evaluating the effect of an intervention, based on components proven to be efficient in other Nordic settings. The X:IT study directs students, their parents, and smoking prevention policies at the schools. These elements have proven to be effective tools in preventing smoking among adolescents. Program implementation is thoroughly evaluated to be able to add to the current knowledge of the importance of implementation. X:IT creates the basis for thorough effect and process evaluation, focusing on various social groups. TRIAL REGISTRATION: Current Controlled Trials ISRCTN77415416.