The growth of regional debts produces risks both at the regional level and in the sphere of intergovernmental relations. The article shows that with a low debt burden at a long-term level, the subjects of the Russian Federation are highly differentiated by the level of debt, and even with a decrease in overall debt, a variation of debt load is growing. On the basis of cluster analysis, four groups of the subjects of the Russian Federation were allocated, depending on the variation of the debt burden and the share of social spending in total regional expenditures. It is concluded that the level of debt burden and its dynamics are explained both by the socio-economic factors for the regional development and the quality of budget management in any subject of the Russian Federation. Accordingly, the procedure for the distribution of intergovernmental transfers and budgetary rules should be agreed with the accounting of objective relationships and institutional effects.