This prospective study of 60 stable, HIV-infected children in an economically deprived setting was designed to document anthropometric and micronutrient disturbances. Investigations included CD4+ counts, anthropometry and plasma levels of albumin, transthyretin, retinol-binding protein (RBP), vitamins A, B6, E and B12, and folate, zinc and copper. The median age was 25 months. Thirty-two per cent had mild, 48% moderate and 20% severe clinical features, and 80% were moderately or severely immunosuppressed. Twenty-eight per cent had a weight Z-score <-2.0 and 58% a height Z-score <-2.0. Many children had micronutrient deficiencies: albumin (70%), transthyretin (100%), RBP (85%), vitamins A (80%), B6 (37%), E (37%) and B12 (5%), zinc (20%) and copper (25%). Sixty-two per cent had two or more trace element or vitamin deficiencies. There was a weak association between micronutrient status and disease status. Micronutrient concentrations did not correlate with chronological age, height-for-age or weight-for-age. CRP was elevated in 53% but did not correlate with any of the micronutrient concentrations. Micronutrient deficiencies were more common and micronutrient concentrations lower in children over 24 months of age.