How can EU policies support the development of innovation capabilities in less developed regions? This note examines the mobilisation of the EU’s two major innovation support instruments: the European Structural and Investment Funds (ESIF) and Horizon 2020 (H2020). Using data from Eurostat and European Commission administrative data on ESIF and H2020 funding, we observe a number of salient patterns: While newer member states benefit from higher research and innovation allocations from ESIF, participation in H2020 remains a formidable challenge. Across Europe we find that H2020 participation is closely associated with a number of proxies of the development of national and regional innovation systems. With few exceptions (most notably Slovenia and the Czech Republic) newer member states are characterised by lower overall R&D intensity, their research and innovation systems are less internationalised and most R&D is performed by public research institutions rather than businesses. Based on a review of literature on the determinants of participation in the H2020 (and its predecessor Framework Programmes), the history of today's advanced innovation systems and a consideration of the objectives of, modes of intervention of and possible complementarities between ESIF and H2020 we single out international collaboration and business innovation capabilities as important instrumental objectives for development-minded policy.