Background South Africa has a persistent burden of sexually transmitted infections (STIs). Male circumcision has been shown to be effective in preventing HIV, and STIs but data are scarce on the protective effect of circumcision in high-risk populations such as migrant miners. The objective of this study was to assess the effect of medical and traditional circumcision on the prevalence of STIs after adjusting for other risk factors in Rustenburg, a mining town in North West Province, South Africa.Methods This cross-sectional study used baseline data collected from a cohort study. Adult males in a mining town were assessed for STIs (gonorrhea, chlamydia, and trichomoniasis) using syndromic assessment. Data on circumcision status and other risk factors for STIs were collected using an interviewer-administered questionnaire. Multiple logistic regression analysis was used to assess the independent effect of circumcision on STI presence after adjusting for confounders. Results A total of 339 participants with a median age of 25 years (IQR 22-29) were included in the study, of whom 116 (34.2%) were circumcised. The overall STIs prevalence was 27.4% (95% CI 22.8% to 32.6%) and was lower in the circumcised participants compared with those who were uncircumcised (15.5% vs 33.6%, respectively, p<0.001). Both medical (OR 0.57, 95% CI 0.34-0.95, p = 0.030) and traditional circumcision (OR 0.34, 95% CI 0.13-0.86, p = 0.022) were strongly associated with a lower risk of STIs after adjustment for employment and condom use. Conclusion In this high-risk population, with a relatively high prevalence of STIs, and 34% circumcision, both medical and traditional circumcision appear to be protective against STIs.