Digital health records can provide advantages to healthcare practice, policy, and research. Several countries have established population-based digitalised data collection, integrated through data linkage techniques. In Lombardy (Italy), a regional population-based registry was established in the 2000s. It collects data from the social and health sector, anonymised immediately after their acquisition and restructured in a single repository. Data can be used for public health interest, planning, monitoring, services evaluation, and research. Indeed, data can also be provided to universities and other scientific institutes. The availability of such data enables to explore the epidemiology of infectious, chronic, and rare diseases. Thus, epidemiological research can support policymakers to tackle public health threats. However, analysis of electronic health records comes along with several challenges, including data inaccuracy, incompleteness, and biases. Researchers should take into consideration limits and barriers related to quality of data. Moreover, health data use must adhere to the national and European privacy legislation, at times limiting the potential of data integration. Therefore, even if big data drives innovation and scientific knowledge, ethical issues regarding privacy should be considered in public debate.