An effective functioning of logistic chains through the use of intermodal transport inevitably necessitates elimination of potential constraints, which have a negative impact on the logistic chains implementation. The objective of the contribution is the analysis, definition as well as classification of constraints related to the logistic chains in the intermodal transport, which should enable to compare levels of constraints in different alternatives of the logistic chain implementation. Based on the comparison of the restriction levels, it is possible to select a more convenient way of the logistic chain implementation. The defined relevant constraints are assessed using scientific methods. These identified constraints have formed the basis for establishing a methodology, which enables to determine weights of constraints as well as to compare their levels on the basis of specific needs of entities.