The cross-sectional study investigated South African rural high school learners' choice of sexual abstinence in order to be able to develop tailored health education messages. All Grade 9 learners from one class at each of 10 randomly selected rural high schools participated. The Integrated Model for Motivational and Behavioural Change was used to elicit attitudes, social influences, self-efficacy and intentions towards sexual abstinence. Chi-square and t-tests were used for bivariate analysis. In total, 454 learners, mean age 16.7 years (standard deviation 1.41) range 14-20 years, participated, of whom 246 (54.2%) were female. When comparing learners reporting abstinence (n = 252) with those not abstinent (n = 202), abstinent learners were significantly more often females (P less than 0.005), younger (16.5 years versus 17.1 years, P less than 0.005) and drank less alcohol (P less than 0.005). Abstaining girls believed that their friends and parents think that they should abstain from sex, that their friends abstained from sex and that abstinence helped them to mature emotionally. Abstinent boys expressed intentions to abstain from sex until marriage. Targeted intervention research is required to encourage South African rural high school learners to delay their sexual initiation to reduce their risk of human immunodeficiency virus infection. Different abstinent messages are needed for boys and girls to address the different patterns of behaviour observed.