Today the most important part of the nations' strategy for innovative development is the elaboration of financing mechanisms for innovative activities. The research tests the hypothesis on the impact of financial performance of innovative companies and the spatial distribution of innovation capital across Russian regions on the effective innovative activity development and presents some elements of the authors' methodology for assessing the amount of innovation capital invested by innovative companies as well as the rate of regions' spatial development. The financial indicators influencing the income of Russian innovative companies are studied based on their financial status analysis; the determinants conditioning the growth of innovative activity within the framework of regional innovation systems, the identification of barriers to innovative capital spillover and the measures for overcoming them in order to develop innovative activities are analyzed. Using the methods of correlation-regression, comparative and graphical analysis, it is analyzed to what extent the individual financial indicators of financing innovative companies influence the final results of the innovative companies' activities. The study reveals a high degree of differentiation in the financial indicators of regional innovative companies and the uneven distribution of innovation capital across the regions of Russia, which inhibits the effective spillover of innovation capital, transfer, diffusion and implementation of innovations. In conclusion, the potential regional centers for innovation capital concentration and areas of developing sources of innovative activity financing are identified.