BACKGROUND Central and Eastern European countries offer opportunities for studying the health effects of historical and present exposures, as well as the transition to a market economy. A prerequisite for research is the availability of good-quality information. This study was undertaken to describe sources of individual data that are available for epidemiological research in Estonia. Particular attention was paid to the methods of operation of health registries. METHODS Information was collected during site visits, interviews with registry personnel and from published reports. For health registries, information was specifically requested on data collection, scope of recorded data, quality control, electronic linkage capability and use of data in research. RESULTS The authors describe 35 data sources containing individual information on vital status, mortality, morbidity, natality and women's health, health and health care, and occupation. The most important health registries are the cancer registry, with data from 1968, and the medical birth registry, with data from 1992. Computerised cause-of-death information is available from 1983. Electronic linkage can be done with most of the data sources, the main matching variable being the eleven-digit personal identification number. Factors potentially affecting data-quality in health registries are undefined legal basis, scarcity of funding and staff, poor acknowledgement of problems, and rare scientific use of registry DISCUSSION Various data sources are available for epidemiological research in Estonia. Thus far, collected data have largely been an under-used scientific resource. In health registries, more attention should be paid to quality control and continuous involvement of researchers.