Innovative development of regions is one of the most acute topics when discussing issues of modern socio-economic development of the country. The problems associated with the evaluation of innovation development of both individual regions and the country as a whole are actively discussed not only in academia, but also in public discourse. Despite the diversity of existing methods for assessing innovation development of territories, the task of forming a scientifically sound system of indicators to assess the level of innovation of regions remains to be solved. The article analyzes Russian and international systems for assessing innovation development of regions. The article considers in more detail the most interesting existing methods, such as the method to assess the innovativeness of the region developed by the Geography Department of Moscow State University, the methodology "Rating of innovation development of the subjects of the Russian Federation" by HSE, the Global Innovation Index, authors' methods of domestic and foreign researchers, which consider a number of indicators characterizing the conditions of formation and implementation of innovation, level of innovation activity, innovation policy effectiveness, human capital, infrastructure, market and business stability, etc. The article reveals the insufficiency of indicators and their validity when they are included in the ratings of innovativeness of regions, which does not allow us to estimate the corresponding level of development of the region objectively. The problems of Rosstat on formation of the list of indicators, characterizing innovativeness of regions, related to limiting the access to the available information in such areas as public service, direct foreign investments, etc., were marked. The purpose of the work is to develop a method for assessing the level of innovation activity of a region. The authors propose a method to assess not only the capacity to increase the level of innovation in the region, but also the effectiveness of using this capacity. The proposed method for assessing the level of innovation development of the region allows deeper and more comprehensive definition of the analyzed level of development of the region on the basis of the research of the innovation potential and effectiveness of its use; it also shows the effectiveness of the state innovation policy implementation at the regional level. This methodology was tested on the example of St. Petersburg.