Despite the need to provide evidence-based health policy, most developing countries suffer from a lack of resources for sound epidemiologic evidence. Most twin registers have been established in developed countries and there are relatively fewer twin registers in developing countries. Considering the immense potential of twin research, it will be worthwhile to attempt to establish a new twin register in Mongolia, where biomedical studies are still scarce. Our objectives were to initiate the process of establishing a nation-wide twin register in Mongolia, based on a nation-wide, population-based database. With the approval and support of the Ministry of Population Development and Social Welfare of Mongolia, we were able to access an initial list of 411 twin pairs who live in the district of Ulaanbaatar, the capital city of Mongolia. By developing a questionnaire to estimate zygosity, we conducted a pilot survey. Those who registered consisted of 822 individuals or 411 twin pairs (same sex: male — 178; female — 157; different sex — 76), two sets of triplets (same sex: female — 2). The age of twins ranged from 1 to 81 (mean age 7.3 ± 11.3), and 52.4% were males. The first twin survey in Mongolia not only resulted in interim data for the Mongolian Twin Register, but has the potential for establishing a larger register by using the national database. It has been proven possible to establish a twin register for research purposes in Mongolia.