f In a comparison of 4 second-generation nucleic acid amplification tests performed with self-collected vaginal swab (SCVS) and first-void urine (FVU) specimens from 575 women, SCVS specimens indicated more infections than did FVU specimens in all assays. The prevalence rates were 9% (53/575 patients) for Chlamydia trachomatis and 2% (11/575 patients) for Neisseria gonorrhoeae. The clinical sensitivities for testing SCVS specimens for C. trachomatis were 98.1% on a Tigris system and 96.2% on a Panther system for the Aptima Combo 2 assay (Hologic Gen-Probe), 98.0% for the RealTime CT/NG assay on an m2000 instrument (Abbott), 90.6% for the ProbeTec CT/GC Q x assay on the Viper system (Becton Dickinson), and 84.6% for the cobas CT/NG assay on the cobas 4800 platform (Roche). Clinical sensitivities for C. trachomatis in FVU specimens were 88.7% (Tigris) and 88.0% (Panther) for the Aptima Combo 2 assay, 76.9% for the RealTime CT/NG assay, 75.5% for the ProbeTec CT/GC Q C hlamydia trachomatis and Neisseria gonorrhoeae infections of the female genital tract present a diagnostic challenge because many patients are asymptomatic (1, 2). This has led to implementation of screening strategies using less-invasive sampling procedures (3, 4), and screening programs often increase the number of samples received in the laboratory (5). Nucleic acid amplification tests (NAATs) for C. trachomatis and N. gonorrhoeae diagnosis have been available from commercial sources for over 15 years. The first PCR assay from Roche was the semiautomated Amplicor CT/NG test (6), which evolved into the automated cobas Amplicor assay. The ligase chain reaction assay (Abbott LCX) was the second NAAT to be used extensively but was withdrawn globally in 2003. A first-generation strand-displacement assay called ProbeTec ET, from Becton Dickinson, became available for evaluation in 1999. During the same time frame, a first-generation transcription-mediated amplification test was developed by GenProbe and evolved into the second-generation Gen-Probe Aptima Combo 2 (AC2) assay, which was evaluated with female specimens and was reported in 2003 (7). More recently, the U.S. Food and Drug Administration (FDA) cleared three additional secondgeneration assays and automated instruments, namely, the Abbott Molecular RealTime CT/NG assay on the m2000 instrument, the Becton Dickinson ProbeTec CT/GC Q x assay on the Viper XTR instrument, and the Roche Diagnostics cobas CT/NG assay on the cobas 4800 instrument.Examination of the package inserts for these newer secondgeneration assays indicated that FDA clearance was granted by comparing the new assays with patient-infected status (PIS) results, with infection being based on positive results from at least two cleared assays when 2 different specimen types were tested.The cobas CT/NG assay was compared with two other secondgeneration assays (AC2 and ProbeTec CT/GC Q x assays) (8, 9). The AC2 test and the first-generation ProbeTec ET assay were chosen for the RealTime CT/NG performance studies (10) and the ProbeTec CT/G...