Sexually transmitted pharyngeal infections due to Neisseria gonorrhoeae (NG) are frequent among ‘men having sex with other men’ (MSM). NG pharyngeal infections are usually characterized by the absence of symptoms, remaining undetected and untreated and, therefore, acting as an important reservoir for the further spread of the infection. Informations about the bacterial composition of the pharyngeal mucosa undergoing a NG infection could help in elucidating the pathogenesis of this condition and could open new perspectives for the prevention, control and treatment of NG pharyngeal infections. In this study, we characterized the pharyngeal bacterial community profiles associated to NG infection in a well-selected cohort of HIV-negative MSM reporting unsafe oral intercourse. A total of 70 pharyngeal swabs were available for the analysis and two groups were compared: non-infected subjects (n=45) and patients with pharyngeal gonorrhoea (n=25).