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To identify the early presence of human papillomavirus (HPV) DNA in the oral cavity of HIV-infected children.The study group comprised 50 HIV-infected children and 50 healthy aged paired controls. Oral mucosa samples were collected by swab, and a 450 bp HPV DNA fragment was amplified by PCR, using degenerate consensus primers directed to the L1 gene. HPV typing was performed using specifics primers for types 6/16 and 11/18.All HPV co-infected children had vertical transmission of HIV. HPV DNA was detected in 6/50 (12.0%) of HIV children and three control group individuals 3/50 (6.0%) (p>0.01). In the HIV group, one had type 11, in the control group one had co-infection of types 11/16, and the others had type 16 and 18.Based upon the results, it is concluded that HPV DNA may be present in HIV disease, but no association with immunosuppression, delivery, or medical records (CD4 cell count, viral load and use of highly active antiretroviral therapy) was observed, and no differences could be observed between the groups either.