In South Africa young women bear a disproportionate burden of HIV infection however, risk factors for HIV acquisition are not fully understood in this setting. In a cohort of 245 women, we used proportional hazard regression analysis to examine the association of demographic, clinical and behavioural characteristics with HIV acquisition. The overall HIV incidence rate (IR) was 7.20 per 100 women years (wy), 95 % confidence interval (CI) 4.50-9.80. Women 18-24 years had the highest HIV incidence (IR 13.20 per 100 wy, 95 % CI 6.59-23.62) and were almost three times more likely to acquire HIV compared to women 25 years and older [adjusted Hazard Ratio (aHR) 2.61, 95 % CI 1.05-6.47]. Similarly, women in relationships with multiple sex partners had more than twice the risk of acquiring HIV when compared to women who had no partner or who had a husband or stable partner (aHR 2.47, 95 % CI 0.98-6.26). HIV prevention programmes must address young women's vulnerability and sex partner reduction in this setting.