The diagnosis of nongenital Neisseria gonorrhoeae infection by the Becton Dickinson ProbeTec ET Chlamydia trachomatis and N. gonorrhoeae Amplified DNA assay had low positive predictive value among an Australian community-based sample of homosexual men. Only 30.4% of oropharyngeal samples and 73.7% of anorectal samples were positive for N. gonorrhoeae by the porA assay. The accuracy of nucleic acid amplification tests in this context is compromised without supplemental testing. © 2008 by the Infectious Diseases Society of America. All rights reserved.