The article considers the problem of the system formation for assessing the effectiveness of the operation of innovation infrastructure facilities, in particular, and various institutional forms of regional innovation infrastructure, in general. The research includes a comparative analysis of various institutional forms of regional innovation infrastructure. Statistical data on infrastructure facilities related to various institutional forms are considered. There is the positive dynamics in the development of innovation infrastructure shown both in the context of individual institutional forms and in terms of individual regions in the paper, also is noted the presence of institutional effects in the development of innovative infrastructure. This is confirmed by the analysis of the geographical distribution of various objects of innovation infrastructure in the Central and Siberian federal districts, which is recorded as uneven and cannot be explained only by factors of the level of regional innovative potential. The existence of the "life cycle" institutional effect is noted, which is confirmed by an analysis of the dynamics of the quantitative characteristics of economic agents related to various institutional forms. A methodology for the formation of a system for assessing the effectiveness of institutional forms of regional innovation infrastructure is proposed, a characteristic feature of which is the relationship between the indicators used and the life cycle stage, which allows comparing the effectiveness of government spending on maintaining the functioning of innovation infrastructure, both within the framework of entities of the same type and between individual institutional forms.