This study hypothesized that human papillomavirus (HPV) infection is associated with increased prostate cancer risk, and that the 40% higher incidence rate in blacks is attributable to a greater prevalence of oncogenic viral DNA in prostatic tissues. Viral L1 and E6 gene sequences were polymerase chain reaction (PCR) amplified in archival tissues from 56 prostate cancer cases and 42 hyperplastic controls. L1 amplimers were hybridized by dot blot to HPV L1 generic probes, as were E6 amplimers to E6 probes specific for HPV 6, 11, 16, 18, 31, 33, and 45. 12.5% of cases and 9.5% of controls were HPV positive by L1 hybridization (age/race adjusted odds ratio = 1.66, 95% confidence interval = 0.33, 8.37). Four of 52 (7.7%) blacks were HPV positive compared to 7 of 46 (15.2%) whites. However, none of the L1-positive samples hybridized to the E6 type-specific probes, and positive results were not replicable using a broader spectrum of PCR primers and probes. These data suggest that HPV infection is not a significant risk factor for prostate cancer and does not explain the excess cancer risk in blacks.