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In this paper, the authors present a novel Web based architecture of a medical registry with enhanced protection of personal data of the patients. The goal of a medical registry is to gather experience from clinical practice concerning a disease or treatment (e.g., hip replacement) and to improve the future treatments by applying adequate methods and selecting optimal products. The processing of health data is strictly regulated by laws protecting patients’ privacy. The presented solution is based on the physical separation of identity related data and clinical data and combining the information from both sources on the screen of the user, according to their permissions. The anonymized clinical data can be used for research whereas the risk of de-anonymizing the patient is significantly reduced. This solution has been verified by an operation of a deployed real-life application.