In today's globalised and highly competitive world, many countries are increasingly reliant on their ability to work with other countries in order to ensure the successful implementation of national priorities. The 'innovate or die' mantra is now supplemented with a 'cooperate or die' mantra. For the countries of the Baltic Sea Region, this is nothing new. Over the past three years, the BSR InnoNet project has succeeded in developing and implementing transnational cluster analysis, capacity building activities, cluster linkages and policy frameworks. On behalf of the BSR InnoNet project, the Nordic Council of Ministers hosted the conference "Innovation and Prosperity in the Baltic Sea Region - New tools for transnational collaboration" on May 7, 2009. This is the conference publication and it has the following three objectives: To present a number of perspectives on the overall rationale for 'cooperating for prosperity' and positioning of the Baltic Sea Region, To present some of the results and tools from the Baltic Sea Region Innovation Network (BSR InnoNet) - which serve as building blocks for continued activities aimed at making the BSR a prosperous place, and To present remaining challenges and visions for the future.