Background. The epidemiology of HPV in men who have sex with men (MSM) in Guangzhou, China, had not been reported previously. Methods. HIV-infected and HIV-uninfected MSM were recruited from a Guangzhou-based MSM clinic in 2013. Sociodemographic characteristics and sexual behaviors were collected. An anal cytological sample was taken for HPV testing. Results. We recruited 79 HIV-infected and 85 HIV-uninfected MSM. The median age was 26 years in both groups. The positivities of anal HPV of any type (81.0% versus 48.2%), any high risk type (50.6% versus 27.1%), any low risk type (55.7% versus 31.8%), and any 9-valent vaccine type (74.7% versus 36.5%) were all significantly higher among HIV-infected compared to that among HIV-negative MSM (p for all < 0.05). The great majority of HPV-infected MSM were infected with 9-valent vaccine types (59 out of 64 HIV-infected and 31 out of 41 HIV-uninfected). Anal bacterial infections were associated with higher anal HPV positivity and greater number of anal HPV types. Conclusion. Sexually active MSM in Guangzhou, especially those infected with HIV, had high and multiple HPV detections. The majority of these cases were potentially preventable by HPV vaccine. Regular anal exams and early HPV vaccination are warranted in this population.