Male circumcision (MC) is reported to reduce human papillomavirus (HPV) prevalence in men. However, the efficacy remains imprecise. The aim of this study was to conduct a systematic review and meta-analysis to assess the relationship between MC and genital HPV infection and genital warts. PUBMED, EMBASE, and Web of Science were searched from inception to March 22, 2015. We identified 30 papers, including a total of 12149 circumcised and 12252 uncircumcised men who were evaluated for the association of circumcision with genital HPV or genital warts. Compared with men who were not circumcised, circumcised men may have had significantly reduced odds of genital HPV prevalence (odds ratio [OR]: 0.68; 95% confidence interval [95% CI]: 0.56-0.82). There was no significant association between MC and genital HPV acquisition of new infections (OR: 0.99; 95% CI: 0.62-1.60), genital HPV clearance (OR: 1.38; 95% CI: 0.96-1.97), and prevalence of genital warts (OR: 1.17; 95% CI: 0.63-2.17). This meta-analysis suggests that circumcision reduces the prevalence of genital HPV infections. However, no clear evidence was found that circumcision was associated with decreased HPV acquisition, increased HPV clearance, or decreased the prevalence of genital warts. More studies are required to evaluate adequately the effect of MC on the acquisition and clearance of HPV infections and prevalence of genital warts.