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Introduction Men who have sex with men (MSM) are at increased risk for human papillomavirus (HPV)-related anal cancer and may benefit from targeted vaccination campaigns, but it is unclear whether vaccination of sexually active MSM still prevents anal HPV infections. Protocolised data on vaccine effectiveness (VE) in routine vaccination programmes targeting MSM are limited. We describe a protocol to evaluate the VE against anal HPV-16/18 infections in young MSM.Methods and analysis This observational study compares HPV-16/18 infection prevalence between vaccinated and unvaccinated MSM of the same age. We recruit MSM at the Sexual Health Center of Amsterdam, born in 1996–2003, who receive bivalent HPV vaccination (Cervarix) (group 1). Participants complete a questionnaire on demographics and sexual behaviour and provide anal, penile, oral gargle and venous blood samples at months 0 and 24. Adverse events are monitored by a questionnaire 2 weeks post vaccine. Recruitment of group 2, also MSM born in 1996–2003, but not vaccinated against HPV, will start 24 months after recruitment of group 1. The same samples are collected, and the same questionnaire is administered. Anal samples are tested for HPV DNA and, if positive, typed for 25 HPV genotypes including HPV-16/18; serum samples are tested for HPV-16/18 antibodies; other samples are stored for future analyses. Type-specific VE will be estimated as 1–OR, where OR refers to the OR of DNA positivity in group 1 at month 24 versus DNA positivity of group 2 for the respective vaccine types. Recruitment of group 1 started in February 2023 and was completed in June 2024. From February 2025 onwards, group 1 will return for the 24-month visit and recruitment of group 2 will start.Ethics and dissemination This study has been approved by the medical ethics committee of the Amsterdam University Medical Center. This protocol presents minimal risk to participants. Findings will be presented to stakeholders in immunisation policy and be disseminated through scientific journals and conference presentations.Trial registration number Clinical Trial Information System 2022-502224-49-00.