Objective: Male circumcision services have expanded throughout Africa as part of a long-term HIV prevention strategy. We assessed the effect of type of service provider (formal and informal) and hygiene practices on circumcision-related morbidities in rural Ghana. Methods: Population-based, cross-sectional study conducted between May and December 2012 involving 2850 circumcised infant males aged under 12 weeks. Multivariable logistic regression models were adjusted for maternal age, maternal education, income, birthweight and site of circumcision. Results: A total of 2850 (90.7%) infant males were circumcised. Overall, the risk of experiencing a morbidity (defined as complications occurring during or after the circumcision procedure as reported by the primary caregiver) was 8.1% (230). Risk was not significantly increased if the circumcision was performed by informal providers (121, 7.2%) vs. formal health service providers (109, 9.8%) [adjusted odds ratio (aOR) 1.11, 95% CI 0.80–1.47, P = 0.456]. Poor hygiene practices were associated with significantly increased risk of morbidity: no handwashing [148 (11.7%)] (aOR 1.78, 95% CI 1.27–2.52, P = 0.001); not cleaning circumcision instruments [174 (10.6%)] (aOR 1.80, 95% CI 1.27–2.54, P = 0.001); and uncleaned penile area [190 (10.0%)] (aOR 1.84, 95% CI 1.25–2.70, P = 0.002). Conclusion: The risk of morbidity after infant male circumcision in rural Ghana is high, chiefly due to poor hygiene practices. Governmental and non-governmental organisations need to improve training of circumcision providers in hygiene practices in sub-Saharan Africa.