The detection and eradication of pharyngeal Chlamydia trachomatis in patients with chlamydial uterine cervicitis (commercial sex workers and others) were investigated. Pharyngeal C. trachomatis was detected in 75.0% of the commercial sex workers and in 21.9% of the other subjects. All the pharyngeal C. trachomatis-positive patients had a past history of orogenital contact. Chlamydial infection was treated with clarithromycin for 7 or 14 days. The presence of C. trachomatis was determined by polymerase chain reaction (PCR) on days 8, 15, and 22 after completion of the treatment. In the 7-day treatment group, the eradication rate of pharyngeal C. trachomatis was 53.3%, 56.7%, and 60.0% on days 8, 15, and 22, respectively, after completion of the treatment, while the eradication rate of cervical C. trachomatis was 83.3%, 96.7%, and 100% on days 8, 15, and 22, respectively. The eradication rate of pharyngeal C. trachomatis in the 7-day treatment was significantly lower than that of cervical C. trachomatis, while there was no significant difference in the 14-day treatment. The eradication rate of pharyngeal C. trachomatis in the 14-day treatment was significantly higher than that in the 7-day treatment. Since the DNA of dead organisms may be detected because of high PCR sensitivity, appropriate therapeutic judgment by PCR could be done around day 22 after completion of the treatment.