This study describes HIV and syphilis bio-behavioral survey conducted among 200 men who have sex with men (MSM) recruited via respondent-driven sampling (RDS) between January 4 and February 1, 2012 in Ulaanbaatar, Mongolia. Participants were administered a structured questionnaire and data were analyzed with RDS-network program in STATA. Of 196 participants who agreed to be tested for HIV and syphilis, 21 (10.7 %; weighted 7.5; 95 % CI: 4.9, 11.4) and 8 (4.1 %; weighted 3.4; 95 % CI: 1.7, 6.7) were positive for HIV and syphilis, respectively. Exposure to HIV prevention programs in the last 12 months was reported by 51.8 % (weighted 33.6; 95 % CI: 27.6, 40.1) of participants. This study found high HIV prevalence and limited uptake of HIV prevention services among MSM in Mongolia. Given the concentrated HIV epidemic among MSM in Mongolia, HIV prevention, treatment and care services should focus on MSM as the population group most affected by HIV.