Men who have sex with men (MSM) are at risk for human papillomavirus (HPV) infection and anal cancer (AC) yet little is known regarding MSM knowledge and risk perception for these outcomes. We surveyed 116 MSM attending a sexually transmitted disease clinic and found that over a quarter (27%) did not know HPV is transmitted via anal sex and most (77%) were unaware of the link with AC. Many MSM (60%) perceived risk for HPV; far fewer (35%) perceived risk for AC. In adjusted logistic regression analyses, having friends or acquaintances with HPV or genital warts was associated with knowledge of anal HPV transmission (odds ratio [OR] = 4.3; 95% confidence interval [CI] = 1.4, 13.4) and AC risk-perception (OR = 6.2; 95% CI = 2.3, 16.7); reporting a regular source of care was associated with awareness of a link between HPV and AC (OR = 3.1; 95% CI = 1.1, 9.1); and MSM and women versus MSM, had less perceived risk for HPV (OR = 0.05; CI = 0.01, 0.29). Nearly all expressed hypothetical acceptance of HPV vaccine. In our sample, many MSM were unaware of a link between MSM sexual practices and HPV-related outcomes.