Rare diseases, including those of genetic origin, are defined by the European Union as life-threatening or chronically debilitating diseases which are of such low prevalence (less than 5 per 10,000). The specificities of rare diseases - limited number of patients and scarcity of relevant knowledge and expertise - single them out as a unique domain of very high European added-value. The legal instruments at the disposal of the European Union, in terms of the Article 152 of the Treaties of the European Union, are very limited. However a combination of instruments using the research and the pharmaceutical legal basis and an intensive and creative use of funding from the First Public Health Programme 2003-2008 and from the Second Health Programme 2008-2013 has permitted to create a solid basis that Member States have considered enough to put rare diseases in a privileged position in the health agenda. The adoption of the Commission Communication, in November 2008, and of the Council Recommendation, in June 2009, and the future adoption of the Directive on Cross-border healthcare, maybe during 2010, have created an operational framework to act in the field of rare disease with European coordination in several areas (classification and codification, European Reference Networks, orphan drugs, European Committee of Experts, etc.). In conclusion, Rare diseases is an area with enormous and practical potentialities for the European cooperation.