Danube Strategy of EU was endorsed by the European Council in June 2011. Eight EU member states and six other countries from the region participate in this programme. The main target is the development of the Danube Region in the areas of obility, energy, environment, elimination of risks, socio-economic challenges and security. No new funds, legislation or institutions have been created. Coordination bodies were constituted and funds supporting further projects within eleven priorities were identified. Here especially 7th Framework Programme of EU, Visegrad Fund, structural funds of EU, national funds and in the future Horizon 2020 are to be mentioned. Danube Region Research and Innovation Fund as a flagship instruments for the unification of national funds is being formed. Scientific community is incorporated via activities of coordinating ministries in the respective countries and via common bodies, like Danube Rectors‘ Conference and Danube Academies Conference constituted under the auspices of European Academy of Sciences and Arts. Academies of Sciences met in 2012 in Smolenice and in Budapest, where they undersigned the Memorandum on Cooperation 2012 – 2017. Also the Center of Excellence ROAD of Slovak Academy of Sciences serves the aims of Strategy. Joint Research Center of European Commission will support the Strategy by collecting basic data as an outcome for the creation of projects and politics. The aims of Strategy are challenging, in terms of improvement the environment, quality of waters, etc., they correspond to the aims of the strategy Europe 2020. First of all the intensity of the Danube River transport should be increased approaching to the exploitation of Rhine. The programme of Strategy cannot be fulfilled without a considerable increase of the activity and success rate of the countries from the region in Horizon 2020 (in comparison with the 7th Framework Programme of EU).