One of the most important aspects of the design activity of passenger railway vehicles is the optimization of the comfort level that is often in contrast with other requirements, such as low weight, to reduce energy consumption, and high and flexible seating capacity. Due to the coach weight reduction, the car body structure becomes more susceptible to structural vibrations that affect the passenger comfort. In modern vehicles, seats are important elements to achieve the desired comfort, but in order to design and estimate the actual comfort level, the whole system must be considered, including the track excitations, a vehicle detailed dynamic model, and the coach and the seat flexibility. This paper describes a numerical model of a double-deck vehicle developed using a MB code that considers measured track irregularities, a detailed vehicle model, and a transfer function of the seat obtained by experimental tests on an optimized seat. In order to make the numerical model more realistic, the coach has been modeled as a flexible body to consider the effect of its natural frequencies. The work has been performed within the "CARITAS" project, whose aim is the design of a high comfort vehicle for people with reduced mobility.