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HIV and alcohol prevention programmes to delay sexual initiation and alcohol use by learners have been shown to be effective interventions in high schools. However, the interplay of the interventions and the background characteristics of learners in preventing sexual initiation and alcohol use have not been examined. In this study, we examine the contribution of background characteristics of learners in HIV and alcohol prevention programme. Data were drawn at two time points from a cohort of 1259 and 1076 grade 9 learners. Generalized linear mixed models were used to predict the effects of background characteristics on alcohol consumption and sexual initiation. The results show that alcohol consumption increased from 34.6% to 39.9% between the two points among the learners. Between the two time points, prevalence of sexual intercourse rose from 31.1% to 37.7%. Background characteristics such as increasing age, being a male, absenteeism from school, importance of religion and average grade point predicted alcohol use. Sexual intercourse was significantly associated with increasing age, being a male, absenteeism from school and importance of religion. The study concludes that HIV and alcohol prevention strategy targeting learners should take serious consideration of their background characteristics for a more effective intervention programme.Keywords: Alcohol, HIV, sexual risk behaviours, learners, South Africa