Background Household characteristics are important influences on the risk of child death. However, little is known about this influence in HIV-endemic areas. We describe the effects of household characteristics on children’s risk of dying in rural South Africa.

Methods We use data describing the mortality of children younger than 5 years living in the Agincourt health and socio-demographic surveillance system study population in rural northeast South Africa during the period 1994–2008. Using discrete time event history analysis we estimate children’s probability of dying by child characteristics and household composition (other children and adults other than parents) (N = 924 818 child-months), and household socio-economic status (N = 501 732 child-months).

Results Children under 24 months of age whose subsequent sibling was born within 11 months experience increased odds of dying (OR 2.5; 95% CI 1.1–5.7). Children also experience increased odds of dying in the period 6 months (OR 2.1; 95% CI 1.2–3.6), 3–5 months (OR 3.0; 95% CI 1.5–5.9), and 2 months (OR 11.8; 95% CI 7.6–18.3) before another household child dies. The odds of dying remain high at the time of another child’s death (OR 11.7; 95% CI 6.3–21.7) and for the 2 months following (OR 4.0; 95% CI 1.9–8.6). Having a related but non-parent adult aged 20–59 years in the household reduces the odds (OR 0.6; 95% CI 0.5–0.8). There is an inverse relationship between a child’s odds of dying and household socio-economic status.

Conclusions This detailed household profile from a poor rural setting where HIV infection is endemic indicates that children are at high risk of dying when another child is very ill or has recently died. Short birth intervals and additional children in the household are further risk factors. Presence of a related adult is protective, as is higher socio-economic status. Such evidence can inform primary health care practice and facilitate targeting of community health worker efforts, especially when covering defined catchment areas.