Ischemic heart disease (IHD) remains one of the most important disorders associated with disability and mortality worldwide, and is one of the major causes of cardiovascular diseases in Mongolia. The objective of the current study was to determine the prevalence of IHD and its related factors in a general population in Mongolia. We conducted a nationwide cross-sectional survey between March and September, 2009. General participants were recruited from urban to rural regions in a multistage random cluster sampling method. The diagnosis of IHD was based on the Rose questionnaire (World Health Organization) and electrocardiographic findings. A total of 369 (16.2 %) subjects with IHD were diagnosed among 2,280 participants. The prevalence of subjects with IHD was significantly increased by age: from 9.9 % in individuals age 40-44 years compared to 17.7 % in those over 60 years. Smoking habits (former and current) and non-frequent intake of fruits and vegetables were significantly positively associated with IHD in men, while heavy alcohol drinking habits and lower education period of time were significantly positively associated with IHD in women. IHD was found to be prevalent, especially among people aged over 40 years, in Mongolia. Statistical factors related to IHD were found to be significantly different based on sex. The current data may provide relevant information to prevent IHD in the Mongolian population.