The effects of railway car-body flexibility on the dynamic analysis of high-speed trains traveling on bridges are studied. The flexible car-body is modeled as a uniform beam supported by the primary and secondary suspensions. A parametric sensitivity study is carried out to examine the effects of different parameters, namely the track irregularity, rail joint, traveling speed and the wheel flat, on the dynamic responses of the car-body and bridge. The rail surface roughness is regenerated by its power spectral density. Different types of rail joint geometries and wheel imperfections are mathematically modeled and included in the numerical simulation. It is found that the flexural mode shapes of the body structure can remarkably affect the calculated ride comfort index especially in the low frequency range.