Eighty-nine tissue specimens from the urinary tract and prostate were analyzed for the presence and physical state of BK virus (BKV) DNA. Large T antigen gene sequences were amplified by PCR from prostate, kidney, ureter, and bladder with prevalences ranging from 50 to 83%. Sequence analysis of PCR products from the high variable BKV regulatory region showed that these tissues contained a new BKV strain (URO1). URO1 presents a duplication of part of the 68- and 39-bp elements of the viral enhancer, and a 68-bp deletion spanning part of the 39- and 63-bp enhancer elements. Six neoplastic specimens (11.5%), but none of the control tissues, contained viral DNA in amounts detectable by Southern blot hybridization (P < 0.05). The tumors positive by Southern blot hybridization harbored rearranged and/or integrated DNA sequences whose size was apparently incompatible with assembly into a viral particle. A full-length, macroscopically intact BKV early region was amplified from these tumors by PCR. The restriction pattern of the rearranged sequences was simple, suggesting that tumors were clonal and that DNA rearrangement occurred at an early stage of neoplastic initiation or progression.