We assessed HIV and STI prevalence, risk behaviors and factors associated with HIV infection in men who have sex with men (MSM) in Guayaquil, Ecuador. Respondent-driven sampling was used to recruit 400 MSM in 2011-2012. Participants completed a computer-assisted self-interview and provided blood samples. Statistical analysis accounted for differential probability of selection and for recruitment patterns. HIV prevalence was 11.3 %, HSV-2 30.2 %, active syphilis 6.9 % and hepatitis B 1.2 %. In the previous 12 months, 84 % of MSM reported casual male sex partners and 25 % sex work. Only 48 % of MSM consistently used condoms with male partners and 54 % had ever been tested for HIV. Of 17 % of MSM reporting a female partner, consistent condom use was 6 %. HIV infection was associated with age 25 or older, active syphilis and homosexual self-identification. Findings suggest continuing HIV risk and a need to strengthen prevention and testing among MSM.