The performance of nucleic acid amplified tests (NAAT) for Chlamydia trachomatis at the cervix and in urine was examined in 3,551 women, and the impacts of clinical findings (age, endocervical and urethral inflammation, menses, and gonococcal coinfection) were assessed. Ligase chain reaction (LCR) and first-generation uniplex PCR were studied relative to an unamplified DNA probe (PACE2) and to an expanded, independent diagnostic reference standard. Relative to the expanded standard, cervical or urine LCR was generally the most sensitive test in most subgroups. Increased detection by NAAT of cervical C. trachomatis over PACE2 was highest among women without mucopurulent endocervical discharge versus those with (relative increase in positivity with cervical LCR, 46%) and among women >20 years old versus younger women (relative increase in positivity with cervical LCR, 45%). The sensitivity of cervical PCR was highest when mucopurulent endocervical discharge was present (84%) and highest for cervical LCR when cervical gonococcal coinfection was detected (91%). Urethral inflammation was associated with higher sensitivities of urine LCR (86 compared to 70% when inflammation was absent) and PCR (82 compared to 62% when inflammation was absent). Menses had no effect on test performance. The effects of patient characteristics on test specificities were less pronounced and were closely related to observed sensitivities. These findings support expanded use of NAAT for screening and diagnosis of C. trachomatis in diverse clinical populations of women.Genital infection with Chlamydia trachomatis is the most commonly reported bacterial disease in the United States and has well-established adverse effects on the reproductive health of women (4, 23). Nucleic acid amplification tests (NAAT), including PCR, ligase chain reaction (LCR), strand displacement assay, and transcription-mediated amplification, are more sensitive for the diagnosis of C. trachomatis than culture, nonamplified DNA probe, and antigen detection tests and maintain relatively high specificity (1, 2). Equally important, the ability to perform NAAT on urine and self-collected vaginal swabs has expanded opportunities for screening men and women (7,10,11,14,21,26,28,29).Our understanding of the clinical manifestations of chlamydial infections in women, including endocervical and urethral inflammation, has been based largely on studies using non-NAAT for detection of infection. Similarly, selective screening criteria for identifying cervical chlamydial infection have been based on risk factors as defined by various non-NAAT. NAAT, however, can detect the presence of fewer chlamydial elementary bodies than non-NAAT (1). Accordingly, among men with urethral chlamydial infection, NAAT demonstrate the greatest increase in sensitivity over non-NAAT in asymptomatic men without urethral inflammation (22). One possible explanation for this is that the quantity of elementary bodies appears to correlate directly with signs of inflammation in men and women and with the prese...