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Spending on innovation activities was increasing in Russia during 2000th, yet there is a strong differentiation between regions in their innovation results. The main aim of the work was to assess innovation systems’ efficiency for the Russian regions according their patent activity, using data envelopment analysis (DEA). The main hypothesis was that efficiency is low in most Russian regions and it was declining during 2000th because of inefficient public R&D expenditures. On the basis of theoretical and empirical background analysis, we proposed several recommendations for RIS (regional innovation system) efficiency assessment by DEA. It was identified that several regions with the largest agglomerations (Moscow, Saint Petersburg, etc.) are the efficiency leaders.