As a result of structural reform of Russian railways, a host of agents that provide customers with loading resources, especially wagons for transport by railway. These processes reduce in efficiency of the car fleet, increasing transportation costs, shortage of cars for many customers, an increase of empty runs and, as a result, a depletion of a number of sections of the network carrying capacity at a reduced total volume of rail traffic. The article describes the reasons for this situation due to the mismatch occurred heterogeneity of rolling stock to existing planning conditions and tariffs. It is also shown that the inefficiency of decentralized car fleet contributes to the predominance of tree-type network, and the importance of this factor in the new environment has increased substantially. To ensure the efficient operation of rail transport as a systemic industry, providing mass-haul transport, it is proposed for integration into a regional logistics. Freight terminals regional logistics transportation and distribution system (RLTRS) is appropriate to create on the basis of major freight railway stations. Thus, the adaptation of planning car traffic volume and train formation to modern standards, the establishment of tariff incentives and long-term changes in network configuration are considered as a prerequisite for the transformation of local transport and technological systems on the network of Russian railways into the integrated transport and logistics systems.