The paper describes the assessment of data on the innovation development of individual countries and regions, taking into account a large number of different indicators. An overview of international and national approaches to the assessment of innovative development is presented: Global Innovation Index (Cornell University, INSEAD, and the World Intellectual Property Organization); Portfolio Innovation Index (USA). The mathematical apparatus for calculating each of them is given. The generalized groups of indicators included in each index are described. Designations and methods of calculation are given to a uniform form of presentation. A methodology for assessing the heterogeneity of the innovative development of countries/economic regions of innovation systems based on the use of clustering methods is proposed. The methodology of the compilation of three indices is given, taking into account the results of clustering and evaluating the qualitative proximity of the studied territorial entities.