The obligations of the country to the WTO at the subfederal level were considered in the article. Their classification has been carried out. Special economic zones, check points at the border, transport tariffs and transit are as among the regional-level obligations. The article has identified the obligations lying within the competence of the regions, i. e., in the support of agriculture, life and health protection, government procurements and price control. Furthermore, subsidizing in industry and agriculture is considered in more details. Subnational government in subsidizing R&D can hardly violate the country's WTO obligations, since the arrangements within the EEU are more strict in comparison with the WTO norms. The Kaliningrad and Magadan areas, the Republic of Crimea and the city of Sevastopol are viewed as disadvantaged regions with unlimited opportunities for their support. However the legislation went the way of trying to modify the special economic zone mode. It is our viewpoint that the exemption of export duties for Kaliningrad enterprises will not be considered as a subsidy in the WTO, but this mechanism has not been not involved. In what concerns the agricultural support, the regions pay little attention to the so-called green-box subsidies. The share of the subfederal level in direct payments to agricultural producers makes 72 % (2012). The share of the subfederal level in 2012 was 28 % of the total amount of ’green’ and nonspecific support. Regional support almost completely is attributed to the ’amber box’. The regional part in the existing share of the agricultural support from the budgets of two levels has to be reduced. The regions of the Russian Federation should develop subsidizing according to green-box programs, which is where product-specific subsidies need to be transferred.