Pharyngeal chlamydial and gonococcal infections can occur as a consequence of oral sex, and they also can be transmitted from the pharynx to the genital tract of sex partners. There have been many reports on the prevalence of pharyngeal Chlamydia trachomatis and Neisseria gonorrhoeae in men who have sex with men; however, there have been few reports on the prevalence of these pathogens in the pharynges of heterosexual men. In this study, we determined the prevalence of pharyngeal C. trachomatis and N. gonorrhoeae in 42 heterosexual men diagnosed with urethritis. Pharyngeal swabs and first-voided urine specimens were tested using the Gen-Probe APTIMA Combo 2 transcription-mediated amplification assay. The prevalence of pharyngeal C. trachomatis and N. gonorrhoeae in patients with urethritis was 2.4 % (1/42) and 11.9 % (5/42), respectively. Among patients with either chlamydial or gonococcal urethritis, 9.1 % (1/11) and 25.0 % (5/20) had pharyngeal C. trachomatis or N. gonorrhoeae, respectively. Our results suggest that screening for pharyngeal colonization by N. gonorrhoeae and C. trachomatis using validated nucleic acid amplification tests should be performed in heterosexual men diagnosed with urethritis.