The article presents themethodology proposalof comprehensive evaluation of the providedservices quality inregional passenger rail transport. The proposed methodology of the quality evaluation can be used for comparing the integrated transport systems by the quality level. It can be utilized as an evaluation of the provided services in the relationship with the submitter and the supplier as well. The methodologyproposal fully accept the transport policy of the EU, specifically the White Paper 2011–The Roadmap to a Single European Transportation Area-Towards a competitive and resourceful efficient transport system, that are also included in the quality norms and transportation operational programme in Horizon 2020.