The molecular evaluation of the chlamydial major outer membrane protein (MOMP) gene (omp1) can facilitate epidemiologic investigations of this pathogen. Genotyping of omp1 provides a more precise characterization of Chlamydia trachomatis than do current immunotyping techniques. Genetic omp1 variants of serovars that are responsible for ocular disease in Tunisia were identified. Archival conjunctival samples collected during 1972 and 1975 from trachoma patients in Douz were sequenced by automation along with additional B and Ba trachoma and genital isolates. Over 90% of the nucleotide changes resulted in an amino acid substitution. Different amino acid sequence changes in variable segments 1, 2, and 4 were found in the specimens collected in 1975 from those collected in 1972. Determination of omp1 genotypes responsible for trachoma will be useful for prospective, epidemiologic studies to identify chlamydial reservoirs within the host, evaluate transmission patterns, and determine the antigenic variation of MOMP for rational vaccine development.