Regional innovation is becoming the main factor in economic growth. The success of the innovative development of a region determines the competitiveness of the territory and well-being of the citizens living in it. The results of the innovative development of regions are statistically observable and measurable; for the assessment, various methods are used, including various indicators in different groups. The innovative development of a region is largely determined by the innovative development of the enterprises located in the region (other measurement problems). There is still an active discussion of the objectivity and correctness of these assessments. The article provides a comparative analysis of the methods for assessing the innovative development of regions used in the EU, USA, Russia and proposed by scientists. The authors studied twenty-eight methods, representing twenty points of view on the structure of indicators for assessing innovative development. It was revealed that most of the methods use from three to five groups of indicators, but without sufficient justification for the selection of these groups; the groupings are, as a rule, based on the “process approach” (which includes three stages: “input”, “process”, “output”), there are no indicators of the effectiveness of the innovation process, many indicators are scattered across different groups (for example, “financing”), which complicates the final assessment of the innovation process. There is no detailed definition of the concept of innovative development, the goals, objectives, criteria are not “spelled out” (perhaps this is considered optional for clarification, or generally understood). The article proposes to clarify the essential content of the concept of “innovative development of a region” as a balanced innovative state of the region, its innovative consistency, specifies the goals, objectives, and assessment criteria. A new architecture of indicators of innovative development of a region is proposed, which includes five groups of indicators: an assessment of innovative potential (the first is an assessment of the educational potential, the second is an assessment of the scientific potential), an assessment of efficiency (third), an assessment of the effectiveness of innovative development (fourth) and the formation and implementation of the regional innovation policy (fifth). The proposed architecture of indicators of innovative development presupposes the implementation of the principle of balanced management: a region forms innovative potential and uses it in an efficient manner (a balance of opportunities and resources); effective regional innovation policy is a balance “regulator”.