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Because warts are often found in the male urethra, human papillomavirus (HPV) may well be present in urine of patients with urethral condylomata.To detect HPV DNA in urine specimens of men with condylomata acuminata using polymerase chain reaction.Forty-seven urine specimens and 25 paraffin-embedded tissues of condylomata acuminata were obtained from men. Of the 47 urine specimens, 29 were from patients with urethral condylomata, 3 from patients with penile condylomata only, and 15 from control subjects without condylomata. Both L1 consensus primers and type-specific primers for HPV 6, 11, 16, 18, and 33 were used.HPV DNA was detected in 22 of the 29 (76%) urine specimens from patients with urethral condylomata, in none of the 3 urine specimens from patients with penile condylomata, and in none of the 15 controls. Paraffin-embedded tissues of all 25 condylomas were positive for HPV DNA. The HPV types detected in urine were identical to those detected in urethral condylomas.HPV DNA is present in urine of patients with urethral condylomata. Urine may be used for noninvasive screening of asymptomatic HPV infections of the male genital tract. Detection of HPV DNA in urine may be useful for monitoring the response to treatment of urethral condylomata.