The study analyses the coordination and synergy effects between three major EU instruments: the 7th Research Framework Programme (FP7), the Competitiveness and Innovation Programme (CIP); and the Structural Funds (SF). The most important potential synergies appear between SF and FP7 and SF and CIP, the main opportunities being based on the thematic complementarities between the programmes with a stronger ‘technology’ or ‘sectoral’ focus. Potential synergies mainly depend on the bottom-up process of selecting strategic objectives in the SF Operational Programmes during which the combination of more than one funding source should be internalised at a planning stage. The major overlap appears in the support for research infrastructure under SF and FP7. More effective co-ordination and reasoned approach to R&D infrastructure investments and support to regional innovation strategies are needed. A risk of overlapping of actions in favour of inter-regional networking was also identified in the field of research and innovation policies and notably clusters. The main gaps appear in support measures for SMEs not being the ‘top technology pioneers’ that could benefit from greater integration in trans-regional co-operation on technology development. To improve the coordination between the instruments the study recommends: the allocation of sufficient resources in the Operational Programmes of the SF to sustain and develop ‘regional research and innovation strategic frameworks’; a major cross-cutting evaluation of inter-regional network funding; and the inclusion in the evaluation studies of the three programmes of an analysis of inter-relations with other instruments.