Innovation is plagued by duplicated efforts, wasted resources and different stakeholder agendas. There is a need for an overarching strategy to bring various research efforts in line with one another, while still preserving regional flexibility and competitive practices. The 'Towards a European innovation ecosystem: research and innovation strategies adapted to national and regional contexts' (EIS 2011) project was funded by the EU to begin developing such a strategy through the conference 'Towards a European Innovation Ecosystem: Research and Innovation Strategies'. Policymakers, academics, industry stakeholders and members of civil society participated and gave their input. Their discussions covered how to tailor strategies for regional and national contexts, and how to achieve a balance between specialisation and diversification. Other topics included how to build participation and synergies between sectors, and how to improve on tools to guide future decisions. Key outcomes included the importance of communication and retaining scientific talent. It was also concluded that the development of regional excellence is a must and that governance and policy need to become more information-driven. Participants of EIS 2011 agreed that the conference was relevant and facilitated a much needed discussion. Since the outcomes will be used to inform policy, this event has made a significant contribution to promoting coordination and cooperation in research and innovation.