The optimal methods for the diagnosis of pharyngeal Neisseria gonorrhoeae infection are uncertain. The objective of this study was to define the performance of culture and nucleic acid amplification tests (NAATs) for the diagnosis of pharyngeal N. gonorrhoeae. In this cross-sectional study, males and females >15 years old who acknowledged performing fellatio or cunnilingus (in the previous 2 months) were recruited from three clinics (two human immunodeficiency virus clinics and one sexually transmitted diseases clinic) located in Birmingham, AL. The test performance of culture for N. gonorrhoeae, the Gen-Probe Aptima Combo 2 transcription-mediated amplification assay (TMA), the BD ProbeTec ET amplified DNA strand displacement assay (SDA), and the Roche Cobas Amplicor PCR was defined by using a rotating "gold standard" of any positive results by two or three of the three tests that excluded the test being evaluated. A total of 961 evaluable test sets were collected. On the basis of a rotating gold standard of positive results by two of three comparator tests, the sensitivity and the specificity were as follows: culture for N. gonorrhoeae, 50.0% and 99.4%, respectively; PCR, 80.3% and 73.0%, respectively; TMA, 83.6% and 98.6%, respectively; and SDA, 93.2% and 96.3%, respectively. On the basis of a rotating gold standard of positive results by three of three comparator tests, the sensitivity and specificity were as follows: culture for N. gonorrhoeae, 65.4% and 99.0%, respectively; PCR, 91.9% and 71.8%, respectively; TMA, 100% and 96.2%, respectively; and SDA, 97.1% and 94.2%, respectively. In conclusion, currently available NAATs are more sensitive than culture for the detection of pharyngeal gonorrhea in at-risk patients. PCR is substantially less specific than culture, TMA, or SDA and should not be used for the detection of pharyngeal gonorrhea.In the latter part of the 1990s, testing for Neisseria gonorrhoeae genital infections was revolutionized by the introduction of nucleic acid amplification tests (NAATs), which achieve sensitivities greater than those of traditional culture methods and which also allow the use of simplified means of specimen collection. For testing of specimens from genital sites, these tests have been found to be preferred by patients (because specimens can be collected less invasively) and by clinicians (because of the ease of specimen collection and increased sensitivity) and permit expanded screening both in traditional clinical settings and at outreach sites where testing has not typically been performed. At present, however, there are few published data on the performance of NAATs commercially available in the United States for the diagnosis of N. gonorrhoeae infections at nongenital sites of exposure.Recent data suggest that oral-genital sexual contact is relatively common and may be increasing among Americans, particularly adolescents and young adults (7,15,17,18). The importance of the oropharynx as a potential site of infection is further emphasized by a recent population-based s...