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BACKGROUND: An important component of the World Health Organization’s comprehensive trachoma elimination strategy is the provision of repeated annual mass azithromycin distributions, which are directed at reducing the burden of ocular chlamydia. Knowledge of characteristics associated with infection after mass antibiotic treatments could allow trachoma programs to focus resources to those most likely to be infected with ocular chlamydia. METHODOLOGY/PRINCIPAL FINDINGS: We monitored 12 communities in rural Ethiopia that had received 3 annual mass azithromycin treatments as part of a cluster-randomized trial for trachoma. One year after the third treatment, a random sample of children from each village received conjunctival examination for follicular trachomatous inflammation (TF) and intense trachomatous inflammation (TI), conjunctival swabbing for chlamydial RNA and DNA, and a household survey. The primary outcome for this study was RNA evidence of ocular chlamydia, which we detected in 41 of 573 swabbed children (7.2%, 95%CI 2.7-17.8). In multivariate mixed effects logistic regression models, ocular chlamydial RNA was significantly associated with ocular discharge (OR 2.82, 95%CI 1.07-7.42), missing the most recent mass azithromycin treatment (OR 2.49, 95%CI 1.02-6.05), having a sibling with ocular chlamydia (OR 4.44, 95%CI 1.60-12.29), and above-median community population (OR 7.81, 95%CI 1.56-39.09). Ocular chlamydial infection was also independently associated with TF (OR 3.42, 95%CI 1.56-7.49) and TI (OR 5.39, 95%CI 2.43-11.98). CONCLUSIONS/SIGNIFICANCE: In areas with highly prevalent trachoma treated with multiple rounds of mass azithromycin, trachoma programs could consider continuing mass azithromycin treatments in households that have missed prior mass antibiotic treatments, in households with clinically active trachoma, and in larger communities.