The diagnosis of rare diseases is often challenging for physicians, but can be supported by Clinical Decision Support Systems. The MIRACUM consortia, which includes ten university hospitals in Germany, develops a Clinical Decision Support System to support the diagnosis of patients with rare diseases. The users are involved in different phases using a user-centred design process. This publication has the objective to summarize the results of all studies performed in context of the requirements elicitation and to derive concrete requirements for the development of the system. Several studies were performed for requirements elicitation: a cross-sectional survey, expert interviews and a focus group. Participants were experts in rare diseases of the MIRACUM locations. 32 requirements were derived and implemented in a prototype. The prototype allows similarity analyses as a decision support functionality by comparing patients without a diagnosis to patients with a rare disease. In the final evaluation, the prototype was rated with a good usability. Since the system is limited in its functionality, further work and improvements are necessary to make it ready for clinical usage.