The objective of this study was to estimate and analyze the costs of treating children with HIV/AIDS at a university hospital in São Paulo, Brazil. The study collected and analyzed data from 291 medical records of children treated at the hospital as of March 2002. The costs of treatment were estimated for each category of patient (exposed and infected) and severity, based on the quantity of inputs and procedures used in treating each child, based on the cost accounting system used at the hospital. The total cost of treatment for children exposed to the HIV was R$ 956.41 and for those infected with HIV R$ 8,092.71 per year. The mean cost of ambulatory care was R$ 6,047.28 for children with severe conditions, R$ 3,714.45 for those with light/moderate conditions, and R$ 948.63 for the exposed. Hospitalized children had annual costs of R$ 19,353.34, R$ 18,823.16, and R$ 871.03, respectively. The medication was a major factor in the cost of treatment. Our estimates are comparable to the findings from other studies, but lower than corresponding findings from the international literature.