BACKGROUND: The overall number of cancer cases is increasing and, therefore, strengthening cancer prevention has become a priority. The institutions responsible for its control establish guidelines for primary prevention. These include recommendations, such as: not smoking, following a healthy diet, doing daily physical exercise or avoiding overweight. Adolescence is a period of adoption and/or consolidation of health behaviors, and both school- and family-based interventions have proven effective to improve them. Furthermore, online and mobile phone educational interventions are encouraging. Consequently, the main aim of this study is to assess the efficacy of an intervention in which these requirements (school, family, the Internet and SMS) are combined to prevent behavioral cancer risk. METHODS: This protocol describes the design and implementation of a complex online program that includes a randomized controlled trial put into practice in two countries: Spain and Mexico. Adolescents and adults of their environment (relatives and teachers) who voluntarily participate will be randomly assigned to the experimental group or to the control group once they have completed the online pre-test. The experimental group members will have free access to a tailor-made and interactive website (http://www.alertagrumete.com). During the academic year, this website will be periodically updated with different school and leisure activities related to the avoidance of risk behaviors. To encourage participation, the program includes a competition that gives rewards to the winners. SMS are also sent to students to stimulate the adoption of healthy behaviors and as a reminder of participation. Finished the intervention, an online post-test is performed in both groups and the impact on the risk behaviors is therefore assessed. DISCUSSION: The program is pioneer, since it combines many components which have already proven effective in previous researches. Moreover, it aims to compare efficacy in two countries with different socio-economic levels to find out if these approaches are equally effective in countries with a lower income level. However, the vertiginous evolution of the Internet and mobile phones may make this tool less attractive for adolescents, who may prefer social networks and other mobile phone applications which are nowadays massively used by their peers. TRIAL REGISTRATION: ISRCTN27988779.