The purpose of this study was to analyze penile lesions that lacked the histological features of condylomata for human papillomavirus (HPV) DNA. Most of these lesions were detected in men whose partners had an HPV-related lesion. Sequences homologous to HPV DNA were detected in 12 of 84 (14%) lesions using in situ hybridization analysis; nine of these lesions contained HPV 6 or 11. HPV DNA was found in 25 of 26 (96%) penile condylomata, all but two of which contained HPV 6 or 11. Using the highly sensitive polymerase chain reaction (PCR), we also detected HPV DNA in four of 20 (20%) of the penile lesions that lacked the histological features of condylomata negative for HPV by in situ analysis. Most of the lesions that were identifiable only after the application of an acetic acid solution were HPV negative when tested with either technique. We conclude that HPV DNA can be found in penile biopsy specimens that do not demonstrate the unequivocal histological features of condylomata but that the detection rate is much lower than for condylomata even when analyzing tissues in men at high risk for HPV-related lesions by PCR. This study underscores the need for caution when interpreting such tissues and the usefulness of in situ analysis for detecting assumed viral proliferation in noncondylomatous lesions.