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Inclusion of self-collected rectal swabs (SCRS) into existing community venue-based HIV surveillance systems for men who have sex with men (MSM) may provide a feasible method for monitoring human papillomavirus (HPV) vaccine-related outcomes in this population. We measured the prevalence of HPV and anal dysplasia through incorporating SCRS into ManCount, the Vancouver site of the M-Track HIV surveillance system.Participating MSM were provided with a self-collection kit for collection on-site or at a follow-up venue. Swabs were subject to polymerase chain reaction amplification for HPV detection, and cytology slides were reviewed for anal dysplasia. Factors associated with participation were identified through multivariate logistic regression.Of 766 men completing ManCount, 268 (35%) agreed to participate, self-collecting 252 specimens (247 on-site). Of 239 complete specimens, 33.5% did not have detectable β-globin; in the remainder (159 specimens) the prevalence of HPV infection was 62.3% (23.3% HPV type 16 or 18; 38.4% HPV type 6, 11, 16, or 18). In the 62.3% (149) of specimens adequate for cytology, the prevalence of anal dysplasia was 42.3% (HSIL 11.4%, LSIL 18.8%, ASC-US 6.7%, ASC-H 5.4%). Participation was associated with venue type, availability of on-site collection, and other characteristics.SCRS can be feasibly integrated within existing community venue-based HIV surveillance systems for MSM, and may be a suitable method for monitoring the impact of HPV vaccination in this population. However, participation may be influenced by venue type and availability of on-site collection, and adequacy of SCRS specimens may be lower in community venues as compared with clinical settings.