OBJECTIVES: To explore the data sources used in economic evaluations performed on new drugs, and to propose an improved data infrastructure in order to deal with future value-based decision making in health care policy in Japan. METHODS: We systematically reviewed economic evaluation studies of the new drugs which were launched in Japan between April 2006 and March 2011, and which have been priced by the cost calculation method, one of two types of pricing for new drugs in Japan. The “Ichushi” and Pubmed databases were used to find the published articles.  RESULTS: A total of 198 drugs were priced under cost calculation methods in the last 5 years in Japan. Fourteen published articles (9 drugs) were found: 5 CUAs and 10 CEAs (including one that was both CUA and CEA). In all studies, several data from different sources were incorporated. Cost data were estimated by using standard treatment protocols and national price lists for drugs and medical services, or obtained from a limited number of claims data. Efficacy data were obtained from RCTs or clinical trial data mostly conducted in Japan. In 4 out of the 5 CUAs, utility data were used from other studies conducted on non-Japanese samples, and 2 CUAs did not consider transferability issues. Other data, such as epidemiological data, were adopted from overseas as well as Japanese studies; usually mortality rates were from Japanese statistics, while incident rates were from overseas.  CONCLUSIONS: In order to increase quality and efficiency to conduct economic evaluations on new drugs, three steps need to be taken in the data environment: increased accessibility to large cost databases such as the national claims database; establish an epidemiological database; and collect and accumulate utility data in Japanese samples.