HIV establishes reservoirs within the brain, causing damage despite individuals adhering to antiretroviral therapy. The long-term consequences of perinatal HIV infection and early treatment in children remain unclear. Proton magnetic resonance spectroscopy was carried out to assess the effects of HIV on neurodevelopment, at a metabolic level, comparing HIV-positive, HIV-exposed-uninfected (HEU) and HIV-unexposed children at 11 years old. Absolute metabolite concentrations were compared between these groups, through linear regression analysis. Elevated choline levels within two regions of interest suggest putative inflammation in HIV-positive children. A reduction of N-acetyl-acetate in a white-matter region of HIV-positive and HEU children implies axonal damage.