Background: About 15% of adolescents in the Netherlands have mental health problems and many also have health risk behaviours such as excessive alcohol consumption, cigarette smoking, use of drugs, and having unsafe sex. Mental health problems and health risk behaviours may have adverse effects on the short and longer term. Therefore, in the Netherlands there is a considerable support for an additional public health examination at age 15-16 years. The study evaluates the effect of two options for such an additional examination. Adolescents in the 'E-health4Uth' group receive internet-based tailored health messages on their health behaviour and well-being. Adolescents in the 'E-health4Uth + counselling' group receive the computer-tailored messages combined with personal counselling for adolescents at risk of mental health problems. Methods and design: A three-arm cluster randomised controlled trial will be conducted in the Netherlands among fourth-grade secondary school students. School classes are the unit of randomisation. Both intervention groups complete the computer-tailored program during one class session; the program focuses on nine topics related on health behaviour and well-being. For each topic a score is computed that can be compared with the Dutch health norms for adolescents. Based on the score, a message is Discussion: It is hypothesized that at follow-up adolescents in the 'E-health4Uth' group and adolescents in the 'E-health4Uth + counselling' group will show fewer mental health problems and less risky behaviour compared to the control group.