Background Estimates for the HIV/AIDS epidemic from the China Ministry of Health show that the epidemic is spreading rapidly among men who have sex with men (MSM). Respondent-driven sampling (RDS) was adapted in 2009 and snowball sampling was adapted to supplement the number of participants in 2010 and 2011. Interviewer-administered questionnaires and blood tests were conducted to confirm enrolment eligibility of participants. A total of 725 HIV-negative participants were included into the cohort study. The cohort had a HIV incidence density of 5.6 (95% CI: 3.9-7.3)/100 person-years (PY) and a syphilis incidence density of 5.6 (95% CI:3.7-7.6)/100 PY. Age ≤20 years (21-25 years, hazard ratio (HR)=0.32, 95%CI: 0.11-0.95/≥26 years, HR=0.17, 95%CI: 0.05-0.66), having not participated in peer education in the past year (HR=2.96, 95%CI: 1.19-7.35), seeking male sexual partners in a public washroom/park (HR=3.61, 95%CI: 1.03-12.47), being currently infected with syphilis (HR=3.21, 95%CI: 1.31-7.91), having sex partners aged ≥30 years (HR=3.40, 95%CI: 1.11-10.39) and having more than four male sexual partners within the past 6 months (HR=3.34, 95%CI: 1.24-9.04) were found to be risk factors for HIV seroconversion (each P<0.05). Being married (HR=2.38, 95%CI: 1.04-5.46), having not participated in peer education in the past year (HR=2.28, 95%CI: 1.08-4.82), having limited HIV/AIDS knowledge (HR=4.28, 95%CI: 1.94-9.43) and having a sexually transmitted disease infection in the past 6 months (HR=4.74, 95%CI: 1.83-12.30) were identified as factors for syphilis infection (each P<0.05). The incidence rates of HIV and syphilis in Mianyang City reamained high in the cohort of MSM for 36 months. Increased attention should be given to this serious epidemic, and appropriate interventions should be implemented to address MSM-specific issues in order to prevent HIV and syphilis infection in China.