Introduction. The interest in measuring of regional innovation capacity and impact of innovation can be attributed to external factors and as a result of active inclusion of the Russian Federation in the global economic system. When the Russian Federation integrates into the world economic system, there is the task is not only to compare the subjects of the Russian Federation on the level innovative activity among themselves but also to determine the best experience on regional level in Russia. The intention of this paper is to expand knowledge of the attributes of the regional system in Russia and improve approaches for improvement of innovation activity. Empirical analysis. This paper proposes and tests a model of institutional differences to explain the influence of risks factors and economic factors on innovation output at the regional level in Russia. This research identifies the factors that determine of Russian innovative activities on regional level. In this paper were used data of innovative activity of organizations in 83 Russian regions from 2008 to 2012. The article analyzes the following factors that affect the innovation activity at the regional level: regional foreign investment, the availability of special economic zones, the population density in the region, domestic regional product (economic activity of the region), and the level of economic, criminal, and financial risks in the region, investment in fixed assets. The methodology of the study. In this study were used a time series model. The main objective of the analysis is to study the impact of regional foreign investment, the availability of special economic zones, the population density in the region, domestic regional product (economic activity of the region), and the level of economic, criminal, and financial risks in the region, investment in fixed assets on the regional patent activity. Results of research. This paper suggests that foreign investment, population density, economic risks and capital investments have a significant positive impact on innovation activity on regional level in Russia. Conclusions. Implications for research and managerial practice are discussed and the model’s relevance for innovation activities in Russia and other major emerging economies is highlighted.