AbstractBackgroundHuman papillomavirus (HPV) infection is associated with anal cancers and is more prevalent in gay, bisexual, and men who have sex with men (gbMSM), partly due to their vulnerability to HIV infection. Baseline HPV genotype distributions and risk factors can inform the design of next‐generation HPV vaccines to prevent anal cancer.MethodsA cross‐sectional study was conducted among gbMSM receiving care at a HIV/STI clinic in Nairobi, Kenya. Anal swabs were genotyped using a Luminex microsphere array. Multiple logistic regression methods were used to identify risk factors for four HPV outcomes (any HPV, any HR‐HPV, and 4‐ and 9‐valent vaccine‐preventable HPVs).ResultsAmong 115 gbMSM, 51 (44.3%) were HIV‐infected. Overall HPV prevalence was 51.3%; 84.3% among gbMSM living with HIV and 24.6% among gbMSM without HIV (p< 0.001). One‐third (32.2%) had HR‐HPV and the most prevalent vaccine‐preventable HR‐HPV genotypes were 16, 35, 45, and 58. HPV‐18 was uncommon (n= 2). The 9‐valent Gardasil vaccine would have prevented 61.0% of HPV types observed in this population. In multivariate analyses, HIV status was the only significant risk factor for any HPV (adjusted odds ratio [aOR]:23.0, 95% confidence interval [95% CI]: 7.3–86.0,p< 0.001) and for HR‐HPV (aOR: 8.9, 95% CI: 2.8–36.0,p< 0.001). Similar findings were obtained for vaccine‐preventable HPVs. Being married to a woman significantly increased the odds of having HR‐HPV infections (aOR: 8.1, 95% CI: 1.6–52.0,p= 0.016).ConclusionsGbMSM living with HIV in Kenya are at higher risk of anal HPV infections including genotypes that are preventable with available vaccines. Our findings support the need for a targeted HPV vaccination campaign in this population.