The healthcare system in Finland has begun routine collection of health-related quality of life (HRQoL) information for patients in hospitals to support more systematic cost-effectiveness analysis (CEA). This article describes the systematic collection of HRQoL survey data, and addresses challenges in the implementation of patient surveys and acquisition of cost data in the case hospital. Challenges include problems with incomplete data and undefined management processes. In order to support CEA of hospital treatments, improvements are sought from the process management literature and in the observation of healthcare professionals. The article has been written from an information system and process management perspective, concluding that process ownership, automation of data collection and better staff training are keys to generating more reliable data.