Sixty-four samples of urethral cells from male sexual partners of women with genital human papillomavirus (HPV) infection were analyzed for the presence of HPV types 6, 11, 16, and 18 by polymerase chain reaction (PCR) followed by slot blot hybridization. Additional samples from 37 of these subjects were analyzed for the presence of viral cytopathic effects by conventional cytology. By PCR, HPV DNA was detected in 21% (14/64) of samples. By cytology, 16% (6/37) of the samples showed cellular changes consistent with HPV infection. Polymerase chain reaction and cytology results were concordant for presence and absence of HPV in 5 and 28 cases, respectively. Three additional HPV-positive cases were obtained with PCR in the cytologically negative samples. The cytologic abnormalities were found to be associated with the presence of both low-risk HPV types and meatal acetoreactivity. On the contrary, HPV DNA positivity by PCR was unrelated to viral type and peniscopic findings. Urethral HPV infection was detected by PCR in 30% of males with visible penile lesions and in 18% of those without. These results indicate that PCR analysis of urethral samples is a helpful adjunct to cytology for the detection of HPV DNA in absence of cytologic evidence of infection.