The Portuguese Health Service (PNHS) is facing growing challenges. These lead to the analysis and definition of strategic priorities in health innovation. This need can only be answered through an interactive and coordinated action at the global level, with "Innovation Union" strategies in the national and international fields and involving all partners and stakeholders. This paper aims to describe the work developed on the project "Health 2.0: Quality and Innovation in the National Health Service" (QISNS), as well as the key actions, results and conclusions. The success of the ongoing structural reforms in the Portuguese health system requires a real and close coordination between central agencies, scientific societies and academic and civil society, in order to maximize its capacity of development and transformation, as recommended by the European initiative "Innovation Union"[1] in 2010 and 2011. In this sense, analyzing the health innovation involves identifying in advance the public policies of innovation and recognizing the progresses made. The theme of innovation presents an increased relevance considering the current situation in the country, the austerity programme and sustained growth. This project is the result of an association between different entities, from the central state institutions to the health care providers, as well as academic, scientific and the civil society representatives'. In the methodological process that preceded the definition of the Strategic Priorities for Health Innovation, the qualitative and quantitative methodologies were explored and organizations and key players identified from the national focal points and experts from the health system, science, technology and higher education in the studied areas. The adopted methodology was the s-plan road mapping [2], consisting on four workshops. The Strategic Priorities for Health Innovation are shown as an horizontal strategy, based on the innovation strategies of the European Union, adjusted to the Portuguese reality and focused on its National Health Service, imported inputs from international experiences and actual outputs resulting from a thorough and comprehensive added value creation chain in R&D&I (research and development and innovation). The definition and context of these strategic priorities arising from the results obtained during the investigation process, demonstrate the current state of R&D&I, namely: 1. Lack of economic profitability of the R&D&I health chain; 2. Modest transfer of results - translational research; 3. Limited capacity for external financing projects (European / International); 4. Reduced ability to articulate the R&D&I networks and the subsequent limitations in the national and international registration of the patent; 5. Limitations when sharing the results/resources/processes/outputs/optimization and reduced protection of the intellectual and industrial property. These are cross country findings recognizing the innovation to be essential to the economic development, sustainability and continuous quality improvement.