To determine the prevalence of human papillomavirus (HPV) DNA in the male partners of HPV-infected women, assess the concordance of the viral group in the infected pair, define the most affected sites in the male genitalia, and compare diagnostic methods in men. Fifty male, stable sexual partners of women positive for HPV DNA by the Hybrid Capture 2 (hc2) test had material brushed from six different anogenital areas for hc2 testing. One week later, patients underwent classic peniscopy, and the lesions were biopsied for histologic analysis and hc2 testing. The brushings were HPV DNA positive in 35 (70%) of the 50 men: 32% in the high-risk HPV group, 14% in the low-risk HPV group, and 24% in both groups. HPV detection per anatomic site was 24% in the glans, 44% in the prepuce internal surface, 30% in the distal urethra, 24% in the prepuce external surface, 12% in the scrotum, and 8% in the anus. Acetowhite lesions were seen in 44 (88%) of the 50 patients. Overall, HPV DNA was detected in 27 (26%) of the 104 biopsy specimens, but histologic examination showed evidence of HPV infection in only 14 (13.5%) of 104 biopsy specimens. In 3 (6%) of 50 patients, hc2 was positive only in the histologic examination. Overall, the prevalence of detectable high-risk HPV DNA among male partners was 60% (30 of 50). Of the 50 male partners studied, 76% were HPV DNA positive. Histologic examination was an inaccurate method to diagnose HPV DNA infection in men; however, brushings detected HPV in 92.1% of the infected men.