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Considerable variation in the outer membrane protein (ompA) of Chlamydia trachomatis has been uncovered by immunotyping and, more recently, by genotyping. This diversity may assist Chlamydia in evading the human immune system; organisms may have a competitive advantage if they infect a host who has previously been infected only by other strains. If so, a diverse set of strains may attain a higher prevalence in a community than a single strain. We determined the predominant strains of ocular C. trachomatis in trachoma-endemic villages of Nepal and tested the hypothesis that strain diversity is associated with the prevalence of infection.Major outer membrane protein gene sequences of chlamydial isolates were determined from ligase chain reaction-positive eye swab samples collected from 10 villages. The diversity of genovars was determined for each village, using Simpson’s index.Two genovar families (Ba and C) and nine genovars were detected, with a single genovar (C1) comprising more than one-half of the samples. The prevalence of clinically active trachoma was significantly associated with the genetic diversity in a village, controlling for village size and number of samples taken in a village.Genetic diversity of C. trachomatis is associated with the prevalence of infection in a community, consistent with the hypothesis that diversity may be necessary to attain a high prevalence in a community.