The system of indicators to assess the innovative development effectiveness from the standpoint of the region is formed. Developed system of indicators was tested on the case of Tomsk region. The problems of Tomsk region innovative development were identified in the post- crisis period. Innovations and investments do not provide the advanced development of innovative manufacturing. Economic indicators of the innovation sector are lower than the lack of innovation sector, social indicators - are on the same level. There is a general instability of the innovation sector indicators. Similar problems are likely to be common to many regions of Russia and the Russian economy as a whole.
Keywords: innovative sector, effectiveness, method of estimation, system of indicators, Tomsk region, Russia