To assess i) whether there is an independent association between HIV-prevalence and settlement types (urban formal, urban informal, rural formal, rural informal), and, ii) whether this changes over time, in South Africa. We draw on four (2002; 2005; 2008; 2012) cross-sectional South African household surveys. Data is analysed by sex (male/female), and for women by age categories (15-49; and 15-24; 25-49) at all-time points, for men in 2012 data is analysed by age categories (15-24; 25-49). By settlement type and sex/age combinations, we descriptively assess the association between socio-demographic and HIV-risk factors; HIV-prevalence; and trends in HIV-prevalence by time. Relative risk ratios assess unadjusted and adjusted risk for HIV-prevalence by settlement type. All estimates are weighted, and account for survey design. In all survey years, and combinations of sex/age categorisations, HIV-prevalence is highest in urban informal settlements. For men (15-49) an increasing HIV-prevalence over time in rural informal settlements was seen (p = 0.001). For women (15-49) HIVprevalence increases over time for urban informal, rural informal, rural formal, and women (15-24) decreases in urban formal and urban informal, and women (25-49) increases urban informal and rural informal settlements. In analyses adjusting for potential socio-demographic and risk factors, compared to urban formal settlements, urban informal settlements had consistently higher relative risk of HIV for women, in all age categorisations, for instance in 2012 this was RR1.89 (1.50, 2.40) for all women (15-49), for 15-24 (RR1.79, 1.17-2.73), and women 25-49 (RR1.91, 1.47-2.48). For men, in the overall age categorization, urban informal settlements had a higher relative risk for HIV in all years. In 2012, when this was disaggregated by age, for men 15-24 rural informal (IRR2.69, 1.28-5.67), and rural formal (RR3.59, 1.49-8.64), and for men 25-49 it was urban informal settlements with the highest (RR1.68, 1.11-2.54). In 2012, rural informal settlements also had higher adjusted relative risk for HIVprevalence for men (15-49) and women (15-49; 15-24; 25-49). In South Africa, HIV-prevalence is patterned geographically, with urban informal settlements having a particularly high burden. Geographical targeting of responses is critical for the HIV-response.