OBJECTIVE The new commercially available polymerase chain reaction (PCR)-based assay, Amplicor C. trachomatis, was compared with cell culture of C. trachomatis, for the detection of chlamydial urogenital infections. OBJECTIVE To evaluate whether the Amplicor C. trachomatis PCR could improve the diagnosis of chlamydial urogenital infections, compared with cell culture of C. trachomatis considered as the reference method. METHODS A total of 466 men and 290 women attending a sexually transmitted disease (STD) clinic were tested by the Amplicor test in urine in men, and in the cervix and urethra in women, and by cell culture in the urethra of both men and women and in the cervix of the women. RESULTS The prevalence of C. trachomatis was 13.7% by cell culture and 14.4% by the Amplicor test in men, and 3.5% by cell culture and 4.5% by the Amplicor test in women. After resolution of the discrepant results, the sensitivity of culture was 91.4% in male urethral specimens and 83.3% in endocervical and female urethral specimens. The resolved sensitivity of the PCR assay was 92.7% in male urine, 91.7% in endocervical samples, and reached 100% in testing both endocervical and female urethral specimens. CONCLUSIONS This rapid PCR-based assay showed an improvement in quality for diagnosing C. trachomatis infections.