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To understand the stabilization in HIV prevalence in South Africa, and why HIV prevalence has not declined further, despite behavior change and apparently moderate risk behaviors.HIV prevalence and 4 HIV-related sexual behaviors in 15- to 24-year old South Africans and Ugandans were compared, before and during HIV prevalence stabilization and decrease, respectively.According to standard indicators, 15- to 24-year-old South Africans have shown behavior change and have moderate risk behaviors. Yet, the HIV prevalence of South African youth is more than twice the prevalence among Ugandan youth, despite 2 times greater reported condom use and an increase in secondary abstinence among young females. We observed inconsistent use of condoms and an extended age distribution of risk together with age and partner mixing. These increase the cumulative risk beyond indicators which are based on sexual behavior in the last year and condom use at last sexual act. In addition, the extended age distribution of risk together with age and partner mixing, increase the cumulative risk beyond standard indicators which are based on sexual behavior in the last year and condom use at last sexual act.Comprehensive HIV prevention in South Africa needs to be intensified beyond individual age groups for example youth, clearly promote consistent condom use and reduction in sexual partners, and focus on the transmission dynamics including older age groups. This should be based on careful behavioral analysis of the epidemic, which goes beyond standard indicators. This study shows the significant risks beyond apparently improving behavioral indicators in Southern Africa, and helps explains the seriousness of the epidemics in this region.