Background: The Directive 2011/24/EU [OJEU 2011, L88/45] on the application of patient rights in cross-border health care requires the European Commission to support Member States in the development of European reference networks (ERNs). These ERNs are meant to ease the access of patients to highly specialized health care and to facilitate the cooperation at the European Union level in particular medical domains where expertise is scarce, especially in the rare disease area. Methods: The Directive 2011/24/EU [OJEU 2011, L88/45] and the recent Commission Delegated Decision [OJEU 2014, L147/71] as well as the Implementing Decision [OJEU 2014, L147/79] require ERNs and health care providers wishing to join ERNs to have the capacity of developing good practices guidelines. Results: This provision results in a number of challenges but also opportunities for Member States with respect to guideline production. Member States could consider the importance of devoting resources to build efficient systems and capacities for the development and implementation of trustworthy guidelines. Furthermore, they could adopt a cooperative approach to optimize guideline production across countries. Finally, they could promote the establishment of new research governance based on systematically identified research gaps and prioritized as well as communicated research recommendations. Conclusion: Member States are at a decisive point in establishing the details to ensure the transparent and effective functioning of ERNs. Producing explicit plans for the development and use of trustworthy guidelines should be an essential part of this effort.