Our objective was to describe the prevalence of low concentrations of retinol, β-carotene, and vitamin E in a group of HIV-infected Latin American children and a comparison group of HIV-exposed, uninfected children. Our hypothesis was that the rates of low concentrations of these micronutrients would be higher in the HIV-infected group than those in the HIV-exposed, uninfected group. This was a cross-sectional substudy of a larger cohort study at clinical pediatric HIV centers in Latin America. Serum levels of micronutrients were measured in the first stored sample obtained after each child’s first birthday by high-performance liquid chromatography. Low concentrations of retinol, β-carotene and vitamin E were defined as serum levels below 0.70 μmol/L, 0.35 μmol/L and 18.0 μmol/L, respectively. The population for this analysis was 336 children (124 HIV-infected, 212 HIV-exposed, uninfected) aged ≥ 1 to < 4 years of age. Rates of low concentrations were 74% for retinol, 27% for β-carotene, and 89% for vitamin E. These rates were not affected by HIV status. Among the HIV-infected children those treated with antiretrovirals were less likely to have retinol deficiency, but no other HIV-related factors correlated with micronutrient low serum levels. Low concentrations of retinol, β-carotene and vitamin E are very common in children exposed to HIV living in Brazil, Argentina and Mexico, regardless of HIV-infection status.