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Objective Male circumcision reduces the risk of HIV acquisition by approximately 60%. Male circumcision services are now being introduced in selected populations in sub-Saharan Africa and further interventions are being planned. A serious concern is whether male circumcision can be provided safely to large numbers of adult males in developing countries. Methods This prospective study was conducted in the Bungoma district, Kenya, where male circumcision is universally practised. Young males intending to undergo traditional or clinical circumcision were identified by a two-stage cluster sampling method. During the July–August 2004 circumcision season, 1007 males were interviewed 30–89 days post- circumcision. Twenty-four men were directly observed during and 3, 8, 30 and 90 days post-circumcision, and 298 men underwent clinical exams 45–89 days post-procedure. Twenty-one traditional and 20 clinical practitioners were interviewed to assess their experience and training. Inventories of health facilities were taken to assess the condition of instruments and supplies necessary for performing safe circumcisions. Findings Of 443 males circumcised traditionally, 156 (35.2%) experienced an adverse event compared with 99 of 559 (17.7%) circumcised clinically (odds ratio: 2.53; 95% confidence interval: 1.89–3.38). Bleeding and infection were the most common adverse effects, with excessive pain, lacerations, torsion and erectile dysfunction also observed. Participants were aged 5 to 21 years and half were sexually active before circumcision. Practitioners lacked knowledge and training. Proper instruments and supplies were lacking at most health facilities. Conclusion Extensive training and resources will be necessary in sub-Saharan Africa before male circumcision can be aggressively promoted for HIV prevention. Two-thirds of African men are circumcised, most by traditional or unqualified practitioners in informal settings. Safety of circumcision in communities where it is already widely practised must not be ignored.