To determine the extent of nucleotide sequence variation in the major outer membrane protein (MOMP) gene among 27 clinical isolates of Chlamydia trachomatis, the MOMP gene was amplified from 13 strains isolated from the endometrium of patients with pelvic inflammatory disease and high titers of anti-chlamydial antibodies and from 14 strains isolated from the cervix of patients with presumed first-time chlamydial infection. Amplified MOMP variable domain DNA from these isolates was directly sequenced and compared with previously published results. Very little sequence heterogeneity in the MOMP variable domains was found in all 27 clinical isolates, suggesting that MOMP sequence heterogeneity is not often associated with the spread of C. trachomatis to the upper genital tract and is not common in the chlamydial strains in the patient population studied.