The new French case-mix system of hospital payment was adopted in 2004 for public hospitals and in March 2005 for private-for-profit hospitals. Implementing this reform requires a period of transition but the challenges ahead can already be predicted. Prices will have to change before this mode of reimbursement can have any real impact. This requires producing more detailed hospital cost data and using fine measuring tools such as the cost accounting method developed for use in this context. This article describes and analyses the main tools and methods selected to implement the new French prospective payment system.