This study characterized the HIV epidemic among men who have sex with men (MSM) in Quito, Ecuador and contrasted risk patterns with other STI’s. 416 MSM ages 15 years and older were recruited using respondent-driven sampling in 2010-2011. Biological testing and a self-interview survey assessed HIV and STI infections and risk behaviors. Analysis incorporated recruiter-level variables and clustering adjustments to control for recruitment patterns. We identify high levels of HIV (11 %), HSV-2 (14 %) and active syphilis (5.5 %) infections, low levels of lifetime HIV testing (57 %), limited knowledge of HIV and STI’s (<48 %) and limited consistent condom use independent of partner type (<40 %). Sex work was associated with all infections while associations with residential location, how casual partners are met and other variables, varied. Scale-up of behavioral prevention and HIV testing is urgently needed. Interventions should target male sex workers and exploit differential patterns of HIV-STI risk to stay ahead of the epidemic.