The paper presents the application of the Multiple Criteria Decision Aid/Making (MCDA/MCDM) methodology in the assessment of the development of different scenarios for an urban public transportation system (UPTS). This methodology allows considering several conflicting objectives and performing the evaluation process in a comprehensive manner. This approach also corresponds to the holistic philosophy: different aspects (economic, technical, social etc.) and interest groups – stakeholders (operators, passengers, city government etc.). The MCDA/MCDM methodology is specifically customized to the real life case study – urban public transportation system in the city of Cracow (Poland). A family of 10 criteria is proposed to evaluate several solutions (W) for a UPTS in terms of their usefulness and attractiveness for different stakeholders. These criteria take into account: travel time and standard, effectiveness of the fleet use, environment friendliness, the level of integration and reliability of the UPTS, safety and security, the profitability and availability of the UPTS, investment costs. Considering the possible solutions, the 6 alternatives were designed heuristically and compared with the current state (denotation of alternative W0). Based on the analysis, for the final considerations compared with the current alternative, 7 new solutions of the integrated urban public transportation in Cracow were adopted, denoted as: W1 (bus/rail alternative: integration of high-speed agglomeration rail with bus transportation), W2 (rail/tram/bus alternative: integration of high-speed agglomeration rail with tram and bus transport system), W3 (alternative with the underground: integration of the underground with high-speed agglomeration rail and with tram and bus transport system), W4 (tram/rail alternative: integration of high-speed agglomeration rail with tram transport), W5 (Tram alternative: integration of tram transport with bus transport), W5A (tram alternative: sub-alternative to the alternative W5, integration of tram transport), W6 (dual-mode tram alternative: integration of dual-mode tram transport). The variants of the scenarios for the urban public transportation system were generated by VISUM computer macro-simulation software. The computational experiment was carried out with the practical application of different Multiple Criteria Decision Aid/Making methods: AHP (Expert Choice program) and Electre III (software package Diviz).