The FAANs project is designed to engage civil society organisations (CSOs) in a “co-operative research” (CR) activity and in future research agenda-setting on “Alternative Agro-Food Networks” (AAFNs). Five academic institutions and five CSO partners dealing with alternative agriculture and rural development from five EU member states will co-operatively carry out literature review, design and conduct participatory action research including stakeholders (focus group discussions, scenario analysis workshops) on the following issues: a) how AAFNs are defined by social, political, commercial and cultural frameworks involving motives beyond direct material interests in practice, b) how current policies facilitate or impede the development of AAFNs, c) how alternatives may be complementary or oppositional to conventional agro-food networks, d) how AAFNs contribute to regional development, and e) how AAFNs link different types of innovation as a basis to broaden EU research policies on the “knowledge-based bio-economy”. FAAN is a social experiment in science governance through trans-disciplinary engagement of civil society people in research at the earliest stage in the process. This upstream approach will identify further research relevant to AAFNs, in order to inform future research agendas. The project will contribute substantially to the evidence base and the understanding necessary to foster more desirable types of agricultural innovation within the European Community, and we will point out how policy frameworks could better facilitate such improvements. Finally we will evaluate the co-operative research process of FAAN in order to identify the strengths and weakness of CR related to AAFNs. We will compare the applied qualitative research methods to see how valid and reliable they are in this context. A comparative approach of national experiences will help to identify best practises in research methods as well as AAFNs management and policies.