The program of Founding Research Centers for Emerging and Reemerging Infectious Diseases was commenced in 2005 with an outline for Japanese universities and research institutions to establish bilateral collaboration research bases in countries where emerging and reemerging infections are breaking out or will likely break out. So far, six universities and two institutions are participating in the program and ten collaboration bases have been established in six countries (five in Asia and one in Africa). Each research base aims to contribute to the security and safety of the partner and own countries by facilitating better understanding of infectious diseases, technology innovation in diagnosis, therapy and prevention, and human resources development. The experiences of the Reseau International des Instituts Pasteur (RIIP), France, and the Wellcome Trust Southeast Asian Tropical Medicine Research Units (Oxford Network), United Kingdom, which appear to share similar missions, suggest that infectious diseases research that is based on overseas research bases can produce first-time results through the building of long-term mutual trust with the counterparts. By referring to these networks as models, Japan's program should be implemented over the long run but not be based on a short-time perspective. Thus, secure funding is a major issue.