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A relevant problem of scientific research is formalization of the processes of interaction between transportation systems and the region in the context of modern ideas of synergetic approach. The purpose of this article is to develop a methodology for assessing and forecasting the needs of a region for container transport system development. The methodology includes two elements. First is the model for forecasting region's demand for container transportation based on the methods of correlation-regression analysis, index prediction and the Monte Carlo method. Second is the imitation model for assessing the needs of the region in the technical and organizational development of the container system. Organizational development is achieved due to system integration of market players, coordinated management of container flows, which makes it possible to establish the synergistic effect availability.