Background The prevalence of Chlamydia trachomatis and Neisseria gonorrhoeae infections men who have sex with men (MSM) and transgender women (TW) in low and middle income countries is poorly understood. As part of a large intervention trial to reduce HIV and sexually transmitted infection (STI) incidence among MSM/TW in Lima, Peru, we analysed the baseline pre-intervention prevalences of anal and pharyngeal chlamydial and gonococcal infections as well as risky sexual behaviours.

Methods We conducted a cross sectional analysis of 718 MSM/TW enrolled in the Comunidades Positivas and Enhanced Partner Therapy Trial in 2008. Chlamydia trachomatis and Neisseria gonorrhoeae were tested using APTIMA^® Combo2 in pharyngeal swabs and self-collected anal swabs. Based on very low rates found in a pilot study, urethral testing was not undertaken. Behavioral surveys were also conducted using Computer-assisted self interviews.

Results In anorectum and oropharynx, the prevalence of Chlamydia trachomatis infection was 19% (95% CI: 16.1%–22.0%) and 4.8% (95% CI: 3.3%–6.6%) respectively, while the prevalence of Neisseria gonorrhoeae infection was 9.6% (95% CI: 7.5%–11.9%) and 6.5% (95% CI: 4.8%–8.5%), respectively for the same sites. 67% of participants reported receptive anal sex, and 62% reported any unprotected intercourse.

Conclusion We found a high prevalence of rectal and pharyngeal bacterial STIs along with high frequency of unprotected anal intercourse among MSM/TW in urban Lima. Studies to demonstrate the clinical and public health benefits of routine screening and treatment of anal and pharyngeal STIs in MSM/TW should be considered.