Two conventional PCR-enzyme immunoassays (PCR-EIAs) and two real-time PCR assays (LightCycler system; Roche Diagnostics) were evaluated as confirmation assays with cppB and 16S rRNA genes as targets. Of 765 male and female genitourinary and nasopharyngeal specimens positive for Neisseria gonorrhoeae in the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae PCR test (Roche Diagnostics), 229 (30%) were confirmed positive; 13 of these (5.7%) were lacking the cppB gene. Of the 534 samples (70%) that could not be confirmed, 81 (15%) showed a positive crossing point. However, melting curve analysis revealed an aberrant melting temperature in the LightCycler 16S rRNA assay; therefore, these samples were considered non-N. gonorrhoeae Neisseria species. Both of the 16S rRNA assays performed well, with positive predictive values of 99.1% and 100% for the PCR-EIAs and the real-time assays, respectively, and a negative predictive value of 99.8% for both. The cppB assays were compromised by the absence of the cppB gene in 5.7% of the N. gonorrhoeae-positive samples, resulting in negative predictive values of 96.8% and 97.6% for the PCR-EIAs and the real-time assays, respectively. Therefore, the 16S rRNA gene is preferable to the cppB gene as a target for confirmation assays. The melting curve analysis of the real-time assays provides useful additional information.Chlamydia trachomatis and Neisseria gonorrhoeae are the two most common causes of sexually transmitted infections (STI). Infection by these microorganisms can lead to clinical syndromes ranging from mild urethritis to pelvic inflammatory disease. However, both organisms can also cause asymptomatic infections in women and men; these infections can proceed in women to an ascending infection of the fallopian tubes (3,10,14). The outcome of the ascending infection can be reduced fertility, infertility, or even extrauterine pregnancies. Therefore, early diagnosis is necessary to prevent these complications and control the spread of infection.Several studies have shown that nucleic acid amplification tests are superior to conventional tests for the detection of C. trachomatis and N. gonorrhoeae (4,5,8). Because these organisms are regularly found together, the COBAS AMPLICOR Chlamydia trachomatis/Neisseria gonorrhoeae (CA CT/NG) multiplex PCR test (Roche Diagnostics, Mannheim, Germany) provides a useful platform for STI evaluation. An internal control greatly reduces false-negative results. The CA CT component has proven to be a useful diagnostic tool for the detection of C. trachomatis in cervical scraping and urine specimens (13,22,23). The CA NG component, however, lacks specificity, as some non-N. gonorrhoeae Neisseria species (NgNS) (8, 16) and even lactobacilli (23) have been reported to give falsepositive results. Therefore, confirmation by a second, more specific PCR assay is required, especially in low-prevalence communities (8,15,22). This second PCR assay should be convenient and fast to ensure that the delay introduced by required confirmation is kept ...