The database of health insurance is important for the planning, monitoring and evaluation of health care programs. It is also useful for the assessment of health need and exploration of risk factors for diseases. After the implementation of national health insurance program in Taiwan, a large-scale database been collected for administrative and managerial purposes. It may also provide essential information for academic researches. Based on our experiences in the analysis of major disease certification profile of national health insurance program, we describe the applocability, essential characteristics, limitations and future perspectives of national health insurance database.