Objectives Men who have sex with men (MSM) living with HIV are at high risk of infection with high-risk human papillomavirus (HPV), the cause of anal cancer. We assess whether anal HPV DNA detection is related to recent anal sexual activity, what types of anal sexual activity or the persistence of HPV genotypes.

Methods We analysed anal swabs taken at the baseline of a 2-year prospective anal cancer screening study of MSM living with HIV from four HIV clinics in Melbourne, Australia. Anal HPV detection was stratified by age and anal sexual behaviours.

Results 281 anal swabs were included in the analysis. The majority (80%, 95% CI 75 to 84) of men were positive for any HPV; 59% (95% CI 53 to 65) were positive for high-risk HPV (hr-HPV) genotypes; and 31% (95% CI 26 to 36) men were positive for HPV 16 and/or 18 with no significant differences according to age groups (p>0.261). In men who reported no receptive anal sexual activity in the last six months (22%), hr-HPV was found in 53% (95% CI 41 to 65) for no anal sexual activity versus. 60% (95% CI 54 to 67) for anal sexual activity (p=0.320). HPV 16 and/or 18 was found in 26% (95% CI 16 to 38) for no anal sexual activity versus. 32% (95% CI 27 to 39) for anal sexual activity (p=0.320).

Conclusions Anal HPV in MSM living with HIV is detected in the majority of men throughout all age groups. Anal HPV detection remains high even in men reporting no anal sexual activity in the preceding six months.