BACKGROUND: Pharyngeal gonorrhoea is common in homosexual men and may be important in maintaining community prevalence of anogenital infections. METHODS: From 2003, all participants in the Health in Men cohort of HIV-negative homosexual men in Sydney were offered annual pharyngeal gonorrhoea screening by BD ProbeTec nucleic acid amplification (NAAT) assay with supplementary porA testing. Participants self-reported diagnoses of pharyngeal gonorrhoea made elsewhere between interviews. Detailed sexual behavioural data were collected 6-monthly. RESULTS: Among 1427 participants enrolled, 65 study-visit-diagnosed pharyngeal gonorrhoea infections were identified (incidence 1.51 per 100 person-years, 95% CI 1.19 to 1.93) of which seven infections were identified on baseline testing (prevalence 0.57%, 95% CI 0.23 to 1.17%). Almost 85% of study-visit-diagnosed pharyngeal infections occurred without concurrent anogenital gonorrhoea. The combined incidence of study-visit-diagnosed and self-reported pharyngeal gonorrhoea (n=193) was 4.45 per 100 person-years (95% CI 3.86 to 5.12). On multivariate analysis, incident infection was associated with younger age (p-trend=0.001), higher number of male partners (p-trend=0.002) and reported contact with gonorrhoea (p<0.001). Insertive oro-anal sex ('rimming') was the only sexual behaviour independently associated with incident pharyngeal gonorrhoea (p-trend=0.044). CONCLUSIONS: The majority of pharyngeal gonorrhoea occurred without evidence of concurrent anogenital infection, and the high incidence-to-prevalence ratio suggests frequent spontaneous resolution of NAAT-detected infection. The association of pharyngeal gonorrhoea with oro-anal sex indicates that a broader range of sexual practices are likely to be involved in transmission of gonorrhoea to the pharynx than previously acknowledged. Screening the pharynx of sexually active homosexual men could play a role in reducing the prevalence of anogenital Neisseria gonorrhoeae.