The Estonian Genome Center of the University of Tartu (EGCUT) is a research institute of the University of Tartu whose aim is to promote the development of human genetic research, collecting information on health issues and genetics of the Estonian population. The activities of the EGCUT are focused on using the results of the latest genomic research to improve public health and on acting as a developer of personalized medicine in Estonia. The EGCUT has created a longitudinal, population-based database which, in addition to phenotypic and personal data, contains also the biological material (DNA, plasma, leukocytes) of 51, 534 Estonian inhabitants (as of December 31, 2011). This comprehensive database represents about 5% of Estonia’s adult population (over 18 years of age) and is the largest cohort for medical research ever gathered in Estonia as well as one of the largest population based prospective cohorts in Europe. The prospective approach allows to follow changes in the established cohort during the next 25–30 years. The ongoing and future research will provide new insights into the interactions between individual genomic variations, life-style, environmental factors and health. Constant updating of the data retains the actuality of the database for an even longer period of time. The further task is implementation of results from genomic studies in the promotion of public health and in planning the national heath care system. Data about the genetic variation of the patient should be used as an additional source of information besides traditional risk factors (age, sex, etc.) considered for diagnosis and treatment.