A total of 3,023 clinical specimens were tested for Neisseria gonorrhoeae by using COBAS AMPLICOR (CA) PCR and confirmation of positives by N. gonorrhoeae-specific 16S rRNA PCR. The sensitivity of CA plus 16S rRNA PCR was 98.8%, compared to 68.2% for culture. Confirmation of CA positives increased the positive predictive value from 54.8 to 96.6%.For the detection of Neisseria gonorrhoeae, culture is still used by many laboratories. However, recent studies showed that nucleic acid amplification-based N. gonorrhoeae tests (NAATs) are much more sensitive (1,2,4,6,7,10). The Roche COBAS AMPLICOR (CA) N. gonorrhoeae test is probably the most widely used amplification test for N. gonorrhoeae. It was shown that certain strains of N. subflava, N. cinerea, N. flavescens, N. lactamica, N. sicca, and Lactobacillus species may produce false-positive results with the CA N. gonorrhoeae test (3, 4, 5, 9, and Manual for COBAS AMPLICOR Neisseria gonorrhoeae PCR test, version 1.0, Roche Diagnostics) and some other N. gonorrhoeae NAATs (8). Therefore, it is clear that positive results obtained with the CA N. gonorrhoeae test should be confirmed by another test method (2,3,4,8,9). In the present study we evaluated the reliability of N. gonorrhoeae testing in a low-prevalence population, using the CA N. gonorrhoeae test as a screening assay and an N. gonorrhoeae-specific 16S rRNA PCR for confirmation.N. gonorrhoeae PCR and culture were performed on 3,023 specimens from nonselected patients (2,415 female and 608 male) obtained by visiting general practitioners (48%), general hospitals (32%), or venereal disease (VD) clinics (20%). The vast majority of the patients were symptomatic, and 75% of them were between 15 and 35 years of age. Over 95% of the specimens were urogenital swabs, and the remaining 5% were rectal, throat, or eye swabs. Swabs for PCR and culture were sent to the laboratory in 2-sucrose-phosphate medium and in charcoal transport medium, respectively. The CA N. gonorrhoeae PCR (Roche) was tested according to the manufacturer's instructions (Roche Diagnostics manual, version 1). A specimen was considered negative for N. gonorrhoeae if the optical density (OD) was Ͻ0.200 and the OD of the inhibition control (IC) was Ն0.200. The specimen was considered positive for N. gonorrhoeae if the OD was Ն0.200, regardless of the IC result. All specimens with an initial positive result were retested in the CA N. gonorrhoeae PCR, and the result of this repeat CA test was conclusive for the final interpretation of the CA N. gonorrhoeae test. For the 16S rRNA N. gonorrhoeae PCR test, new DNA extracts from the original clinical specimens were prepared. The 16S rRNA N. gonorrhoeae PCR test (Roche) was also performed according to the manufacturer's instructions (manual for Neisseria gonorrhoeae 16S rRNA PCR test, version 2, Roche Diagnostics) and included hybridization with an N. gonorrhoeae-specific probe added to microwell plates. Specimens repeatedly positive by CA N. gonorrhoeae PCR and positive by 16S rRNA N. gonorrhoeae PCR were con...