Characteristics of sexual partnerships, as well as those of the individuals involved, might influence the use of condoms and risk of HIV transmission. We set out to identify characteristics of non-spousal sexual partnerships associated with condom use at last sex in the previous year and HIV infection in the previous three years among sexually active young people in rural South Africa. We conducted an analysis of follow-up data (collected in 2004) from a cohort of 14-35-year old men and women recruited to a cluster-randomised trial. Data on 1647 non-spousal sexual partnerships during the previous year were reported in 2004 and analysed alongside new HIV infections over the previous three years among 762 individuals who were HIV-negative in 2001. Structured interviews elicited information on sexual behaviour. HIV serostatus was assessed through oral-fluid ELISA. Condom use at last sex was reported for 615/1647 non-spousal sexual partnerships (37.3%) and was more commonly reported by individuals who were younger, more educated and aware of their HIV status. Condom use was more common in casual partnerships, those where the male partner was younger, where sex was less frequent and where the respondent believed the partner to have other sexual contacts. New HIV infection in the last three years was identified for 87/762 individuals (11.4%) and was more common among females and those out of school. Infection risk was associated with the age of the partners and was less common among individuals reporting less frequent intercourse in the previous year. Characteristics of sexual partnerships, as well as those of individuals, are important determinants of condom use and risk of HIV infection. Male characteristics may be particularly important because of their greater capacity to make decisions about HIV prevention. Established non-spousal sexual partnerships are an increasingly important context for HIV transmission in this setting.