Over the last 20 years, the participation of lay-people or CSOs in processes of research and innovation has achieved the character of a guiding principle (cf. Epstein 1996; Brown et al. 2004; Frickel et al. 2010; Baldwin/Hippel 2011). CSOs are seen as agents of civil society, which are non-for-profit and oriented towards public’s interests. These involvements are attractive for civil society actors due to the opportunity to be involved in research agenda setting, and for researchers due to the access to specific knowledge and human resources. Accordingly, the European Union Commission perceives participation of civil society actors as a main opportunity for improving processes and impact of research and innovation (Felt/Wynne 2007; Schomberg 2013). Against this background, the purpose of this paper is to show how contemporary modes of Civil Society Organization’s (CSO) participation in the scientific research are working in the European research programmes. Our study is based on a combined empirical study about the inclusion of CSOs on the basis of a quantitative survey of all 14.000+ European Commission FP7 projects in combination with a qualitative case-study analysis of 30 projects. We show that EU’s attempts to mainstream participation in research were quite successful as in 21% of all research projects in its 7th framework program participation activities took place. But we recognize diverging social and cognitive dynamics happening in such projects. We found out that there are six different types of research projects which include CSOs. These types are built on two dimensions, the social interaction form between CSOs and researchers (difference between marginal, balanced and central position of CSO) and the importance of CSOs for knowledge production (difference between focused or transformative). These types and their specific participation schemes as well as their governance challenges will be sketched as will be theoretical and practical consequences arising from them.