While human papillomavirus (HPV) infection is associated with genital warts, anal cancer, and oral cancer, limited research has examined what men think causes these diseases. We sought to examine knowledge and beliefs about HPV-related disease among gay and bisexual men, who are at high risk for HPV infection and HPV-related cancers, and compare them to heterosexual men. We conducted an online survey in January 2009 with a national sample of men aged 18-59 who self-identified as either gay or bisexual (n = 312) or heterosexual (n = 296). The response rate was 70%. Fewer than half of men knew that HPV can cause genital warts (41%), anal cancer (24%), and oral cancers (23%). However, gay and bisexual men typically knew more than heterosexual men about these topics. Overall, most men believed that sexual behavior causes genital warts (70%) and anal cancer (54%), and tobacco use causes oral cancer (89%). Perceived causal factors differed substantially among the three diseases, while differences by sexual orientation were fewer and smaller in magnitude. Many men were unaware that HPV infection can cause genital warts, oral cancer, and anal cancer.