Objectives A human papillomavirus (HPV) vaccination programme targeted towards men who have sex with men who are disproportionately affected by HPV anogenital infection and related disease was established in Scotland in July 2017. We aimed to establish a baseline HPV prevalence to assess the potential impact of the programme.

Methods Residual rectal swabs taken in a sexual health clinic (n=1 248) were tested for the presence of HPV and HPV-type prevalence was collated and stratified by age. Prevalence of HPV types included in the quadrivalent and nonavalent vaccines was specifically assessed.

Results 72.8% (95% CI 70.2% to 75.3%) of swabs were positive for HPV with 59.1% (95% CI 56.3% to 61.9%) of samples positive for at least one high-risk type. A least one of HPV 6, 11, 16 and 18 was detected in approximately half of the swabs. HPV prevalence generally increased with age but did not significantly differ between older age groups. The presence of more than one HPV type increased with age and over half of samples had multiple types present.

Conclusions While HPV prevalence in this population is high, the potential impact of the vaccination programme is substantial given that 50% are not infected with a vaccine type. Defining a preimmunisation baseline in this group will be important for longitudinal monitoring of impact.