Human polyomaviruses JC and BK are ubiquitous in healthy human adults, persist as latent viruses and can be reactivated in the immunodeficient host giving different pathologies. Due to the experimental evidence of their potential oncogenicity and neurotropism, as well as to the enhanced viral production induced by co-infection with HIV-1, a possible role of these polyomaviruses has been suggested in AIDS-associated progressive multifocal leucoencephalopathy (PML) and Kaposi's sarcoma. JCV and BKV DNA was detected by PCR in urine and in peripheral blood mononuclear cells (PBMC) using primers specific for structural (VP1) and regulatory (R) regions. In HIV-positive subjects BKV and JCV sequences were found respectively in 8.1% and 31.6% of urine samples whereas in PBMC the positivity increased to 22.8% for JCV and in 51.1% for BKV. Our results indicated that, at DNA level, the presence of BKV and JCV in urine and PBMC was higher in HIV-1 positive subjects than in HIV-1 negative subjects and that, in contrast with JCV, BKV positivity was inversely related to blood CD4-level. Intravenous drug users (IVDU) showed significant increases in both BKV and JCV positivity, while an increased JCV viruria was found in homo-bisexuals compared to heterosexuals. The high prevalence of viral DNA in PBMC of both healthy and HIV-positive individuals agrees with the hypothesis that lymphocytes may represent a viral latency site permitting the establishment of virus persistence in affected organs, or a vehicle for the spread of the infection to different tissues.