Article 32 (1) of Directive 2012/34/EU provides that in order to obtain full recovery of the costs incurred by the infrastructure manager (IM) a Member State may, if the market can bear this (MCB), levy mark-ups on the basis of efficient, transparent and non-discriminatory principles, while guaranteeing optimal competitiveness of rail market segments. The charging system shall respect the productivity increases achieved by railway undertakings (RUs). The main implementation problem is a question how to evaluate the MCB level, the productivity increases achieved by RUs and optimal competitiveness in an efficient, transparent and non-discriminatory way if: 1) the meanings of the included concepts are unclear for natural monopoly; 2) there are mutual contradictions among these concepts, for instance, obligation to allocate trains „which can pay at least the cost that is directly incurred as a result of operating the railway service…” and a commercial advantage to give priority to the most productive RU when capacity is limited; and 3) it is impossible to make unified methodology for mark-up evaluation due to the differences among EU rail markets. As a result of the study it was concluded that the distinction of market segments in networks with primarily freight transportation appears as a result of the requested deviations from the optimal usage of the rail network.