The article would like to point at the significance and function of social evaluation of S&T and innovation policies/programs along with the possibilities of its application on innovation system and innovation program in Croatia. After brief review of the development of evaluation practices of S&T and innovation policy in the world and in Croatia in the text are presented theoretical concepts in the economy and other social sciences which have influenced their shaping. Theoretical sources of the social evaluation based on social theory of innovation and new innovation paradigm are given. The scope and goals of social evaluation are discussed with the following conclusion: the goal is to determine sociocultural and political factors that make a series of interconnected phenomena which cause “the institutional deficit” of innovation system. The argument is that understanding of these factors within Croatian innovation policy is more significant for the increase of the national innovation capacity than standard economic indicators. Finally a model for social evaluation of Croatian innovation system and policy on the example of HITRA-TEST is proposed.