During the latter half of the 1990s, Japanese healthcare professionals and policy-makers recognized the value of an "evidence-based" approach. At the same time, an increased social awareness of the need to protect research participants and personal information began to appear. Recognition of an evidence-based approach further promoted epidemiologic research while regulations on personal information protection imposed certain limitations on this same research. In April 2000, as a solution to this conflict, a working group funded by Japan's Ministry of Health and Welfare (MHW; currently the Ministry of Health, Labour and Welfare: MHLW) proposed a first draft of ethical guidelines for epidemiologic research. Over the next two years, the collection of domestic and foreign data by working groups and governmental ad hoc committees, questions raised by the mass media, and public statements made by organizations, such as the Science Council of Japan and the Japan Epidemiologic Association (JEA), led to a collaborative effort between the Ministry of Education, Culture, Sports, Science and Technology and the MHLW. This effort led to the creation of the Ethical Guidelines for Epidemiologic Research in June 2002, which was revised in 2004. Furthermore, JEA also announced the Ethical Guidelines for Conducting of Epidemiologic Research in October 2002. While the development of these ethical guidelines has been a challenge for Japanese epidemiologists, it has also allowed the epidemiologic community to understand their role in society. This review aims to provide insight into the interaction between the epidemiologic community and society by assessing historically the developmental process of these ethical guidelines.