Abstract Purpose The core task of European Reference Networks (ERNs) is to reduce health care inequalities throughout Europe for all patients with rare and complex conditions. A secure web-based application for virtual consultations, the Clinical Patient Management System (CPMS), was developed by the EU to provide expert specialized care for all these patients. This review analyses the opportunities and difficulties that the implementation of this virtual network implies for physicians as well as for the patients. Methods European Reference Network on Rare Endocrine Conditions (Endo-ERN) installed an Operational Helpdesk (OH) to support their members in using CPMS. The OH initiated several actions to facilitate and increase the usage of CPMS. Satisfaction with the system and reasons for low participation rates in virtual case discussions were analyzed by different surveys. Results The number of CPMS users increased constantly, but the active usage of the system remains insufficient. Main reasons were technical difficulties, lack of time and insufficient awareness about CPMS in experts and patients throughout Europe. Still, outcomes of the virtual discussions are considered useful by involved experts and the discussions have provided topics for educational webinars and research. Conclusions CPMS is a secure system with many advantages compared to previous ways of consulting experts but also difficulties that need to be overcome with future strategies. By facilitating its use and increasing awareness among all relevant European experts and patients, CPMS can help to make the existing expertise available for all patients with rare (endocrine) conditions throughout Europe as it was intended.