Thirty-six HIV-1 cases had been reported by December 2007 in Mongolia. Therefore, Mongolia has been regarded as a very low HIV-1 epidemic country, although the surveillance system is not fully developed. The aim of this study was to evaluate the risk status of HIV-1 infection in Mongolia. A total of 1415 blood samples from high-risk populations including female sex workers, men who have sex with men, mobile men, tuberculosis patients and male sexually transmitted infection (STI) clinic clients and 1050 samples from healthy controls were collected. The seroprevalences of anti-HIV-1/2, anti-Treponema pallidum, hepatitis B surface antigen (HBs Ag), anti-hepatitis C virus and hepatitis B surface antibody in the high-risk populations were 0%, 23.1%, 15.5%, 8.0% and 48.2%, and those in the controls were 0%, 3.1%, 14.7%, 4.4% and 44.4%, respectively. HIV-1 prevalence is currently low. However, according to the high prevalence of STIs in the high-risk populations, the risk status for HIV-1 infection is estimated to be high.