The paper is focused on the proposal regarding the regional transport organization within Integrated Transport System in a given territory using the selected multi-criteria analysis methods. Introductory parts of this research study include basic information related to this topic as well as description of the current state of the public passenger transport operation, specifically the Integrated Transport System, on a particular territory. Subsequent part of the paper consists of specification of all the data and methods used and applied to obtain the final outcomes. The most important part of the paper highlights all the acquired results and proposed recommendations that need to be established to achieve the more appropriate regional transport organization in the examined territory.