BACKGROUND: Literature is limited on the effects of high prevalence HIV on fertility in the absence of treatment, and the effects of the introduction of sustained access to antiretroviral therapy (ART) on fertility. We summarize fertility patterns in rural northeast South Africa over 21 years during dynamic social and epidemiological change. METHODS: We use data for females aged 15-49 from the Agincourt health and socio-demographic surveillance system (1993-2013). We use discrete time event history analysis to summarize patterns in the probability of any birth. RESULTS: Overall fertility declined in 2001-2003, increased in 2004-2011, and then declined in 2012-2013. South Africans showed a similar pattern. Mozambicans showed a different pattern, with strong declines prior to 2003 before stalling during 2004-2007, and then continued fertility decline afterwards. There was an inverse gradient between fertility levels and household socioeconomic status. The gradient did not vary by time or nationality. CONCLUSIONS: The fertility transition in rural South Africa shows a pattern of decline until the height of the HIV/AIDS pandemic, with a resulting stall until further decline in the context of ART rollout. Fertility patterns are not homogenous among groups.