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Despite substantial progress in the delivery of HIV prevention programs, some communities continue to experience high rates of HIV infection. We report on temporal trends in HIV prevalence in pregnant women in a community in rural KwaZulu-Natal in South Africa.Annual, anonymous cross-sectional HIV sero-prevalence surveys were conducted between 2001 and 2013 among first visit prenatal clinic attendees. The time periods 2001 to 2003 were defined as pre-antiretroviral therapy (ART), 2004 to 2008 as early ART, and 2009 to 2013 as contemporary ART roll-out, to correspond with the substantial scale-up of ART program.Overall, HIV prevalence rose from 35.3% [95% confidence interval (CI): 32.3 to 38.3] pre-ART (2001–2003) to 39.0% (95% CI: 36.8 to 41.1) in the early ART (2004–2008) to 39.3% (95% CI: 37.2 to 41.4) in the contemporary ART (2009–2013) roll-out periods. In teenage women (<20 years), HIV prevalence declined from 22.5% (95% CI: 17.5 to 27.5) to 20.7% (95% CI: 17.5 to 23.8) and to 17.2% (95% CI: 14.3 to 20.2) over the similar ART roll-out periods (P = 0.046). Prevalence increased significantly in women 30 years and older (P < 0.001) over the same time period largely because of survival after ART scale up. Teenage girls with male partners of age 20–24 and ≥ 25 years had a 1.7-fold (95% CI: 1.3–2.4; P = 0.001) and 3-fold (95% CI: 2.1 to 4.3; P < 0.001) higher HIV prevalence respectively.Notwithstanding the encouraging decline in teenagers, the ongoing high HIV prevalence in pregnant women in this rural community, despite prevention and treatment programs, is deeply concerning. Targeted interventions for teenagers, especially for those in age-disparate relationships, are needed to impact this HIV epidemic trajectory.