BACKGROUND: Low caste adolescent girls living in rural northern Karnataka are at increased risk of school drop-out, child marriage, and entry into sex-work, which enhances their vulnerability to HIV, early pregnancy and adverse maternal and child health outcomes. This protocol describes the evaluation of Samata, a comprehensive, multi-level intervention designed to address these structural drivers of HIV risk and vulnerability. METHODS/DESIGN: The Samata study is a cluster randomised controlled trial that will be conducted in eighty village clusters (40 intervention; 40 control) in Bijapur and Bagalkot districts in northern Karnataka. The intervention seeks to reach low caste girls and their families; adolescent boys; village communities; high school teachers and school governing committees; and local government officials. All low caste (scheduled caste/tribe) adolescent girls attending 7th standard (final year of primary school) will be recruited into the study in two consecutive waves, one year apart. Girls (n = 2100), their families (n = 2100) and school teachers (n = 650) will be interviewed at baseline and at endline. The study is designed to assess the impact of the intervention on four primary outcomes: the proportion of low caste girls who (i) enter into secondary school; (ii) complete secondary school; (iii) marry before age 15; and (iv) engage in sex before age 15. Observers assessing the outcomes will be blinded to group assignment. The primary outcome will be an adjusted, cluster-level intention to treat analysis, comparing outcomes in intervention and control villages at follow-up. We will also conduct survival analyses for the following secondary outcomes: marriage, sexual debut, pregnancy and entry into sex work. Complementary monitoring and evaluation, qualitative and economic research will be used to explore and describe intervention implementation, the pathways through which change occurs, and the cost-effectiveness of the intervention. DISCUSSION: This is an innovative trial of a comprehensive intervention to improve the quality of life and reduce HIV vulnerability among marginalised girls in northern Karnataka. The findings will be of interest to programme implementers, policy makers and evaluation researchers working in the development, education, and sexual and reproductive health fields. TRIAL REGISTRATION: ClinicalTrials.Gov NCT01996241 . 16th November 2013.