Introduction Data regarding extra-genital Neisseria gonorrheae (NG) and Chlamydia trachomatis (CT) in men who have sex with men (MSM), and transwomen (TW) in Latin America is limited. We determined the prevalence of pharyngeal, rectal, and urethral NG and CT among MSM, and TW and associated risk factors and behaviours.

Methods We used data from the Expedited Partner Therapy Screening Study of men who have sex with men (MSM) and transgender women (TW) in Lima, Peru. Participants completed a CASI survey regarding socio-demographic data, sexual risk behaviours, and STD symptoms. Anal and pharyngeal swabs and urine specimens collected by the study physician were tested for CT and NG using NAAT (Aptima GenProbe).

Results We screened 834 participants (551-gay identified men, 264 heterosexual/bisexual men and 19 TW) for CT and NG between October 2012 and July 2014. The median age of participants was 27 years (range 18–70). CT prevalence was 3.5% in urine, 4.5% in pharyngeal and 15.6% in rectal specimens. NG prevalence was 2.7% in urine, 9.4% in pharyngeal and 8.3% in rectal specimens. Approximately 75% of participants with rectal infections reported no symptoms in the previous 30 days. More than 92% of extra-genital CT infections and 83% of extra-genital NG infections were identified in participants with negative urine test results. Younger age was strongly associated with increased prevalence of both pharyngeal NG (p = 0.054) and rectal CT (p = 0.008) and NG infections (p = 0.002). Receptive anal intercourse was associated with higher prevalence of rectal CT infection (p = 0.012). Pharyngeal NG (p = 0.005) was more frequent in participants reporting multiple partners.

Conclusion Extragenital CT and NG infection is highly prevalent, usually asymptomatic and in a majority of cases, associated with negative urine tests among MSM and TW in Peru. Routine screening at multiple anatomic sites using NAAT should be performed.