Nanotechnology innovation has peculiar characteristics. This paper reviews the methodology and results, drawn from cases analyzed on two EU projects: EULASUR and EULACERMAT. The cases covers both European and Latin American experiences, particularly from Mercosur countries. We analyze specifically nanotechnology innovation based on new and advanced materials. The main conclusion of this paper is that innovation in advanced materials, based on nanotechnology, relies crucially on networks of cooperative agents. It starts from the validated assumption that innovation is interactive in nature. Therefore, it is needed to co-create through the participation to obtain feasible results. The position of advanced materials within the related (new or existent) value chains explains to a great extend the border conditions for innovating in this nanotechnology field. It appeared clearly that innovation in this field is a complex problem, with the same degree as researching (nanoscience), and that the connections between them were not obvious nor simple. Concerning policy implications, it is useful to discriminate them in terms of the temporal horizon of what type of nanotechnology innovation should be promoted, particularly for developing countries’ trajectories, for ensuring that the impacts of advanced materials will be suitable for the society.