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HIV-1 RNA PCR is a widely available and sensitive assay but has not been studied for use in early diagnosis of HIV-1 infection in infants.Research HIV-1 DNA PCR and HIV-1 RNA PCR were performed on peripheral blood mononuclear cells and plasma, respectively, from 284 blood samples from 204 infants. A commercially available HIV-1 quantitative RNA PCR was also performed on plasma from the 132 samples from HIV-1-infected infants and 22 of the samples from HIV-1-uninfected infants.Sensitivities of all assays varied with infant age. HIV-1 DNA PCR had a sensitivity of 27% in the ≤3-week age group (n = 11) whereas qualitative and quantitative RNA PCR had sensitivities of 64 and 55%, respectively (P not significant). Each assay had a sensitivity of 96.2% at 4 to 6 weeks (n = 26) and 100% at ≥7 weeks of age (n = 95). Specificity of HIV-1 DNA PCR for all age groups was 100%, whereas specificities of qualitative and quantitative RNA PCR assay were 96.1 and 95.5%, respectively.HIV-1 RNA PCR may offer a slight advantage in sensitivity over DNA PCR in the diagnosis of HIV infection in young infants. Positive RNA results can be found in a small number of infants who are not HIV-1-infected. HIV-1 RNA detection should not be routinely used alone for the diagnosis of HIV infection in young infants.