In Japan, the National Clinical Database (NCD) was founded in April 2010 as the parent body of the database system linked to the board certification system. Registration began in 2011, and to date, more than 3,300 facilities have enrolled and more than one million cases are expected to enroll each year. Given the broad impact of this database initiative, considering the social implications of their activities is important. In this study, we identified and addressed issues arising from data collection and analysis, with a primary focus on providing high-quality healthcare to patients and the general public. Improvements resulting from NCD initiatives have been implemented in clinical settings throughout Japan. Clinical research using such database as well as evidence-based policy recommendations can impact businesses, the government and insurance companies. The NCD project is realistic in terms of effort and cost, and its activities are conducted lawfully and ethically with due consideration of its effects on society. Continuous evaluation on the whole system is essential. Such evaluation provides the validity of the framework of healthcare standards as well as ensures the reliability of collected data to guarantee the scientific quality in clinical databases.