This paper analyses the methods to assess the socio-economic impacts stemming from participation in the EU Research, Technological Development and Demonstration Framework Programmes (FPs) projects. Some of the most significant impacts of Central and Eastern European participation in FPs can only be understood in the context of the changing national innovation systems (NIS). In other words, when assessing impacts, besides the ‘usual’ questions on product and process development, job creation, etc., a broader set of questions should be asked, concerning competences, too: managerial, project development, network and collaboration-building capabilities, i.e. the process, and elements, of organisational learning. Our main methodological argument is based on two underlying characteristics of the Hungarian NIS. First, it had been fragmented in the planned economy era, and the academy-industry relations had been rather weak. Second, due to the overall socio-economic transition, it is also in flux: some former links have been further damaged, while new players have appeared and new, stronger incentives have been put in place to form new partnerships. Behavioural and organisational ‘effects’ of FP participation are thus likely to be crucial – besides the ‘usual’ outputs and impacts. Our main policy conclusion is that it would well worth the effort to apply this broader framework to assess the impacts and effects of PP participation using a larger, statistically representative sample. Thus a reliable description could be obtained, on which basis sound policy conclusions could also be drawn