This article discusses the design of an ongoing cluster-randomized trial comparing two forms of school-based sex education in terms of educational process and sexual health outcomes. Twenty-nine schools in southern England have been randomized to either peer-led sex education or to continue with their traditional teacher-led sex education. The primary objective is to determine which form of sex education is more effective in promoting young people's sexual health. The trial includes an unusually detailed evaluation of the process of sex education as well as the outcomes. The sex education programs were delivered in school to pupils ages 13-14 years who are being followed until ages 19-20. Major trial outcomes are unprotected sexual intercourse and regretted intercourse by age 16 and cumulative incidence of abortion by ages 19-20. We discuss the rationale behind various aspects of the design, including ethical issues and practical challenges of conducting a randomized trial in schools, data linkage for key outcomes to reduce bias, and integrating process and outcome measures to improve the interpretation of findings.