Rare diseases (RD) are diseases that affect not more than 5 per 10 000 persons (according to the EU definition). 7000 distinct rare diseases exist, affecting between 6% and 8% of the population (about 30 million EU citizens). The lack of specific health policies for rare diseases and the scarcity of the expertise, translate into delayed diagnosis, few medicinal products and difficult access to care. That is why rare diseases are a prime example of a research area that strongly profits from coordination on a European scale. At present only few European countries fund research on rare diseases through specific dedicated programmes. Therefore, the funding of transnational collaborative research is the most effective joint activity to enhance the cooperation between scientists working on rare diseases in Europe and beyond. The E-Rare consortium was built to link responsible funding bodies that combine the scarce resources and fund rare disease research via Joint Transnational Calls (JTCs). The current E-Rare-3 project proposal will extend and strengthen the transnational cooperation by building on the experience and results of the previous E-Rare-1&2 programmes. The consortium comprises 26 institutions from 17 European, Associated and non-European countries. Its international dimension will be directly translated into close collaboration with IRDiRC and other relevant European and international initiatives. IRDiRC guidelines and policies will be implemented in the four JTCs and representatives of the IRDiRC Scientific Committees will be invited to join the Advisory Board of E-Rare-3. Members of the EUCERD group will be involved in identifying rare disease research needs. Patients’ organizations from Europe (represented by EURORDIS) and beyond will be invited as a key partner towards collaborative efforts for research promotion and funding. The collaboration with European Research Infrastructures will be consolidated to enhance efficient and participative research.