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Urine samples from 211 community children (3–7 years age), from 33 HIV type-1 infected children and from 56 HIV- negative children were collected and analyzed for the presence of BK virus (BKV) DNA by PCR. PCR amplifications were carried out using primers specific for the BKV structural region VP1. We also investigated the distribution of BKV subtypes by a restriction fragment polymorphism assay (RFLP). We demonstrated BKV DNA in 3.8% of 211 community children with a higher prevalence of subtype I. In HIV-1 positive children we detected BKV DNA in 2 urine samples (6%) out of 33, both belonging to subtype I. The HIV-negative cluster did not show any positivity to BKV DNA. The results confirm a more frequent primary BKV infection in children of 3–5 years of age and a higher prevalence in hospitalized children affected by HIV-1. The most relevant finding was that among both the community and HIV-1 positive children the subtype I was the most frequently detected.