Objectives Understanding of hospital cost is crucial to achieve an ideal balance between the assurance and improvement of patient safety and quality, and efficient use of finite resources. However, neither a standardized calculation methodology nor a large-scale database of costs in acute-care hospitals exists in Japan. This study aims to develop a standardized methodology, construct a nationwide cost database in Japan, analyse the characteristics of the database and examine the relationship between the cost and the charge from the viewpoint of an appropriate reflection of the cost to the price. Method We designed the costing framework, gathered the data for patients discharged from 139 acute-care hospitals in Japan between July 2004 and October 2004 and constructed a database containing information on 284 730 patients. The characteristics of the database and the relationship between the cost and the charge were investigated. Results In the nationwide database we constructed, a wide range in the average cost per hospitalization and average cost per diem was observed. A wide variation of cost components was seen across major diagnostic categories. Moreover, there was a high correlation between the cost and the charge (Correlation coefficient = 0.94). Conclusions After designing a costing framework, a nationwide database comprised of individual case-level costs with components for acute-care hospitals in Japan was successfully developed. We hope this study contributes to appropriate decision making and helps motivate further research geared towards efficient hospital management and a rational payment system in Japan.