OBJECTIVES: To investigate risk factors for ocular Chlamydia trachomatis infection and active trachoma, comparing communities receiving or not receiving an intervention programme of community-wide azithromycin treatment and health education. METHODS: In a 3-year post-intervention follow-up survey, 1722 children aged 3-9 years, from randomly selected households in 37 communities, were examined for signs of active trachoma and had samples taken to test for ocular C. trachomatis by polymerase chain reaction. Multivariate random effects logistic regression analyses considered interventions at community level, adjusting for other independent risk factors as appropriate. RESULTS: Younger age, ocular discharge and flies on eyes were risk factors for active trachoma in communities with and without antibiotic treatment. After azithromycin treatment, odds of active trachoma were lower in children aged 6-9 years than in children aged 3-5 years (OR 0.48, 95% CI: 0.36-0.66) and higher for children with ocular discharge (OR 4.5, 95% CI: 2.6-7.7) or flies on their eyes (OR 2.5, 95% CI: 1.6-3.7). Odds of C. trachomatis infection were lower in children aged 6-9 years than in younger children (OR 0.47, 95% CI: 0.23-0.96); and in children who received 2 or 3 doses rather than 1 (OR 0.26, 95% CI: 0.08-0.88). CONCLUSIONS: In communities that received or did not receive the mass antibiotic treatment, the same risk factors for C. trachomatis and active trachoma were identified. Education and environmental improvements need to supplement antibiotic campaigns in order to positively impact on these remaining child level risk factors.