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Background. Low-Risk Human Papillomavirus (LR-HPV) genotypes 6 and 11 cause genital warts. This study investigated the association of LR-HPV infection with male circumcision (MC). Methods. We used data from the South African MC trial conducted among young men. Urethral swabs, collected among intervention (circumcised) and control (uncircumcised) groups, were analyzed using HPV linear array. Adjusted LR-HPV prevalence rate ratio (aPPR) and Poisson mean ratio (aPMR) of number of LR-HPV genotypes were estimated using log-Poisson regression, controlling for background characteristics, sexual behaviour, and HIV and HSV-2 statuses. Results. Compared to controls, LR-HPV prevalence and mean number of genotypes were significantly lower among the intervention group ((8.5% versus 15.8%; aPRR: 0.54, P