Relationships between, on the one hand, the university and the world of finance and economics, and between basic research and technological applications, on the other, have undergone profound changes, and these have intensified over the last 30 years. Innovation's ability to serve as a foundation for the development of new products, processes and services has come to be seen as a factor determining the success or failure of firms and countries, with innovative capacity depending on the knowledge factor. In recent years studies of innovation systems have expanded considerably, so that there is now an abundant literature, made up of essays, works of empirical observation at various levels (national, regional and sectoral), and some comparative case studies. Out of the various approaches, the following stand out: <p>a) Economics has come to emphasize the so-called &quot;innovation system&quot; which emerged from the evolutionary tendency, the main characteristic of which, in comparison to neoclassical approaches, is the significance it attaches to institutions and learning processes (Nelson and Winter, 1982). </p><p>b) Analysis of public policy covers a number of contributions which focus on the organization and nature of state R&amp;D systems, dealing with the emergence of institutional structures and the dynamics of the relationships between political actors, as well as with the problems of governance they produce (Elzinga and Jamison, 1995). </p><p>c) Sociology also encompasses a variety of approaches to the different processes whereby knowledge is generated and used, such as &quot;mode 2&quot; of the production of scientific knowledge (Gibbons et al., 2008), the Triple Helix approach (Etzkowitz, 2003 and 2008) - in this discipline, this is the approach which has analysed in the most systematic way the systemic characteristics of scientific knowledge in its relationships to politics and productive innovation - and the analytical work of Nowotny (2005), Shinn and Ragouet (2005), Pestre (2003), and Krimsky (2004).</p><p>Existing studies of innovation systems in Spain and Portugal reflect the diversity of models and methodological options available. Research has been undertaken in both countries into concrete aspects of science policy (Sanz and Garcia, 2005; Gon&ccedil;alves, 1993; Cara&ccedil;a, 2003), knowledge production in various sectors of the academic world (Garcia and Martins, 2008; Fern&aacute;ndez Esquinas et al., 2009) and entrepreneurial innovation processes (Oliveira, 2008). There have also been studies which address jointly several aspects of their respective systems (for example, in Spain, Sebasti&aacute;n and Mu&ntilde;oz (eds), 2006; and in Portugal, Godinho, Mendon&ccedil;a and Pereira, 2007). In looking at the situation as a whole, therefore, no exhaustive study has been carried out from a unified analytical standpoint, which would make it possible to observe changing trends in both countries systematically and assess the extent of systematic inter-relationships in innovation processes in the Iberian peninsula and its ultra-peripheral Atlantic archipelagos.</p>