OBJECTIVES: To assess the nutritional status of children in a rural community with high HIV prevalence in rural Uganda and to examine the impact of HIV infection at the individual and population level. Methods Cross-sectional population-based survey of children aged 0-12 in a cohort comprising the residents of 25 neighbouring villages in rural southwest Uganda. Anthropometric indicators of nutritional status (height for age, weight for age and weight for height) were assessed in relation to children's HIV serostatus, maternal HIV serostatus and maternal vital status. Children with a Z score of <-2 were defined as undernourished, with a Z score <-2 for weight for age defining underweight, for height for age defining stunting and for weight for height defining wasting. RESULTS: Of 5951 children surveyed, 91% underwent anthropometric measurement: 30% were underweight, 42% stunted and 10% wasted. HIV seroprevalence among children aged 2-12 was 0.7%. The prevalence of underweight was significantly higher in HIV-positive than in HIV-negative children (52%vs. 30%), as was the prevalence of stunting (68%vs. 42%), but there was no significant difference in the prevalence of wasting (4%vs. 9%). There were no significant differences in the prevalences of indicators of undernutrition in children classified by maternal HIV and vital status. CONCLUSIONS: Chronic childhood undernutrition is common in this rural community. HIV infection had a direct effect in worsening children's nutritional status, but no indirect effect in terms of maternal HIV infection or maternal death. The population-level impact of childhood HIV infection on nutritional status is limited on account of the low HIV prevalence in children. The response to undernutrition in children in Africa requires action on many fronts: not only delivering community-wide HIV and nutritional interventions but also addressing the many interacting factors that contributed to childhood undernutrition before the HIV era and still do so now.