This article considers the changes in the regulatory and support system of agriculture, taking place in Russia as a whole and its territorial entities (evidence from the Altai Territory), in connection with the country’s involvement to the World Trade Organization (WTO). The aim of the current research is to assess the potential effects of the major obligation parameters, accepted by Russia in the field of agriculture within the WTO, on the innovative activity of the agricultural sector. The research methods include an abstract logic technique, dialectic approach, positive and normative analysis, economical and statistical techniques, and others. The necessity for reorientation of the state aid towards maximum impact of “green box” measures, whose capacities are not limited by the WTO rules, is proved based on the analysis of international experience in using various instruments for domestic support of agricultural sector. The study resulted in conclusion that it is “green box” that due to its very nature is capable to ensure to the fullest extent the creation of institutional environment, conducive to the acceleration of innovation processes in the regional agricultural sectors.