Objective To examine the risk factors of malnutrition among children whose mothers are infected with HIV in sub-Saharan Africa (SSA). Methods Multilevel logistic regression models applied to Demographic and Health Survey (DHS) data collected during 2003-2008 from 18 countries in SSA, where the DHS included HIV test data for adults of reproductive age. Results Across countries in SSA, the risk of malnutrition among children whose mothers are infected with HIV is particularly high among children aged one, boys, multiple/twin births, those who were smaller than average at birth, or whose mothers had no education, or in poorest or single parent households. Although these risk factors generally apply to all children from the same communities, the higher risk of child malnutrition among those in the poorest households is amplified among children whose mothers are infected with HIV. Also, while in general children who are breastfed for up to 6months are significantly less likely to be malnourished than those who were never breastfed; the benefit of breastfeeding is not evident among children whose mothers are infected with HIV. Conclusion Contextual community/country HIV prevalences show interesting patterns: the risk of malnutrition among children whose mothers are infected with HIV is lower in countries with higher HIV prevalence. These findings have important implications for interventions to address malnutrition among children made vulnerable by HIV/AIDS in the SSA region. © 2011 Blackwell Publishing Ltd.