The purpose is to determine the prevalence of drug-resistance mutations in HIV-1 infected children under antiretroviral treatment from Brazil. Blood samples from sixty one human immunodeficiency virus type 1 (HIV-1) vertically-infected Brazilian children are studied. DNA was extracted from the samples, and a 1.0 kb fragment containing HIV-1 PR and RT-coding sequence were amplified by Nested Polymerase Chain Reaction sequencing. The HIV-1 sequencing, based on the polymerase gene sequences (protease and reverse transcriptase regions), was as follows; subtype B (83.6%), subtype F (9.8%) and B/F viral recombinant forms (6.6%). Two major protease inhibitor-resistance associated mutations, M36I and L90M, were most prevalent in our samples (32.8%), as well as the polymorphism L63P (42.6%). Many mutations associated with reduced susceptibility to nucleoside or nonnucleoside reverse-transcriptase inhibitors were detected: M184V (42.6%), M41L (37.7%), D67N (26.2 %), T215Y (24.6%), L210W (21%). 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