Our purpose was to investigate the human papillomavirus (HPV) type distribution using the Hybrid Capture 2 (HC2) Microplate assay in males. We tested a urethral swab from 550 HIV-negative males with genital warts and 64 HIV-negative males clinically free of genital warts, partners of HPV-infected females, using the HC2 Microplate assay. A perianal swab was also obtained from patients with perianal warts. In the first group, HPV DNA of any type was detected in 280 (50.9%) patients. Relatively few patients with urethral or perianal warts demonstrated a negative test (both P < 0.0001). Low-risk types were commoner, accounting for 60.0% of the HPV cases, high/intermediate-risk types accounted for 23.6%, while 46 men (16.4%) were infected with both types. Of 13 subjects (20.3%) of the second group who tested positive for HPV DNA, 61.5% were infected by low-risk types, 23.1% by high/intermediate-risk types and 15.4% had a dual infection. In conclusion, male partners of infected females and males with genital warts are predominantly infected by low-risk HPV types, but a substantial proportion is also or only affected by high-risk types.