Chlamydia trachomatis infects the urogenital tract and eyes. Anatomical tropism is correlated with serovars which are characterized according to the variation in the major outer membrane proteins encoded by the ompA gene. The aim of the present study was to determine the distribution of C. trachomatis serovars among patients with follicular conjunctivitis in Iran. A total of 68 conjunctival specimens from symptomatic adults were studied for the presence of C. trachomatis using polymerase chain reaction (PCR) analysis. Serovars were determined by Omp1 PCR-RFLP analysis. C. trachomatis was detected in 38 (55.9%) of patients with follicular conjunctivitis, with higher C. trachomatis prevalence in the younger age groups. Twenty-six (38.2%) of these patients had a history of urinary tract infection. Four distinct serovars were identified in the conjunctiva samples using molecular genotyping. The most prevalent was serovar E, followed by G, I, and F. Our serovar distribution indicated that chlamydial follicular conjunctivitis usually has a genital source. Genital serovars may cause eye diseases, especially in sexually active adults. On the other hand, conjunctivitis might be the only sign of sexually transmitted infection. Therefore, genotyping C. trachomatis in ocular and genital specimens could be beneficial for acquiring more detailed epidemiological information about the etiology of the disease and monitoring treatment success.