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To estimate the prevalence of antibodies to HPV16 and HPV18, and genital HPV DNA among MSM attending a London sexual health clinic, to inform the potential benefit of vaccination in a high risk population.A cross-sectional study of 18-40 year-old MSM including a computer-assisted self-interview for behavioural data, and collection of extra-genital and intra-anal swabs, and blood. Anogenital samples were tested for 21 genotypes of HPV DNA using an in-house assay. Blood samples were tested for anti-HPV16 and HPV18 IgG by ELISA.496 MSM were included: among HIV negative MSM, HPV16 seroprevalence was 27% (95%CI 23–31) and HPV18 was 16% (13–20); HPV16 and 18 DNA prevalence 12.6% (9.8–15.9) and 6.0% (4.0–8.5) respectively. In HIV-positive MSM, seroprevalence was 58% (95% CI 37–77) and 35% (95%CI 17–56), and DNA prevalence 29.6% (13.8–50.2) and 11.1% (2.4–29.2) respectively.After adjusting for age and lifetime partners, seropositivity for anti-HPV–16 and/or HPV–18 was associated with: HIV-positive diagnosis (HPV16-aOR: 3.16 [95%CI 1.37–7.28]), receptive anal sex in the last three months (HPV16-aOR: 3.39 [2.01–5.71]; HPV18-aOR: 2.14 [1.18–3.90]), use of drugs anally (HPV18-aOR: 2.07 [1.05–4.10]) and anogenital same-type DNA detection (HPV16 aOR: 3.58 [2.05–6.23]; HPV18 aOR:2.71 [1.17–6.27]).Anogenital HPV DNA detection was less frequent than, but strongly associated with same-type HPV seropositivity. Most MSM attending a sexual health clinic had no serological or DNA evidence of exposure to HPV infection. This supports the case for the potential benefit of targeted HPV vaccination of MSM attending sexual health clinics, as currently being piloted in England.