Background. Data on iron and vitamin A deficiency are scarce in school-aged children living with HIV (HIV+) compared with children without HIV (HIV–). Both deficiencies can contribute to anaemia. Objective. To assess anaemia, iron and vitamin A status in a sample of HIV+ and HIV– school-aged children in South Africa. Methods. In this comparative cross-sectional study, biomarkers for anaemia (haemoglobin), iron (plasma ferritin (PF), soluble transferrin receptor), vitamin A (retinol-binding protein (RBP)) and inflammatory status (C-reactive protein, α-1-acid glycoprotein) were measured in 8 - 13-year-old children from Cape Town living with (n=143) and without HIV (n=148). Measurements of PF and RBP were adjusted for inflammation using a regression-correction approach. Results. HIV+ children had higher prevalences of anaemia (29% v. 14%; odds ratio (OR) = 2.6; 95% confidence interval (CI) 1.4 - 4.9; p=0.002), iron-deficient erythropoiesis (20% v. 9%; OR=2.5; 95% CI 1.2 - 5.0; p=0.013) and iron deficiency anaemia (11% v. 4%; OR=2.9; 95% CI 1.1 - 7.7; p=0.035) than HIV– children. Marginal vitamin A deficiency was noted in 52% of HIV+ and 57% of HIV– children (p=0.711). Subclinical inflammation was more prevalent in HIV+ than HIV– children (p=0.012). Conclusion. Anaemia, iron-deficient erythropoiesis and iron deficiency anaemia were more prevalent in HIV+ than HIV– children. Prevalence of marginal vitamin A deficiency was high in both groups. Efforts to improve micronutrient status and mitigate nutritional determinants of anaemia in HIV+ children from resource-limited settings should be prioritised.