We report prevalence of Treponema pallidum (TP) seropositivity and herpes simplex virus type 2 (HSV-2) infection and risk factors associated with their prevalence in a cohort of men who have sex with men (MSM) in Bangkok, Thailand. Between April 2006 and March 2010 we enrolled Thai MSM into a cohort study based at the Silom Community Clinic, with baseline behavioural data and laboratory testing for sexually transmitted infections (STIs). Logistic regression was used to analyse risk factors associated with the prevalence of TP seropositivity and HSV-2 infection. From a total of 1544 enrolled men (mean age 26 years) TP, HSV-2 and HIV seropositive rates were 4.4%, 20.7% and 21.6%, respectively. After multivariable analysis, participating in group sex, reporting paying for sex, reporting sex with a casual partner in a park and being HSV-2 seropositive were associated with TP prevalence. Age ≥30 years, having less than a high school education, past use of recreational drugs, meeting casual sexual partners at a public venue (sauna) and TP seropositivity were associated with HSV-2 infection. The significant baseline prevalence of TP seropositivity and HSV-2 infection in this cohort demonstrates the need for screening and treatment of these STIs and targeted prevention interventions in Thai MSM in Bangkok.