In this paper, a whole-body vibration analysis using a three-dimensional human biodynamic model is presented, and the dynamic behavior of the body exposed to vibration by a railway vehicle is investigated with respect to ride quality. Since a subject in a railway vehicle is exposed to multi-axial excitation conditions, the acceleration of the body is calculated by summing the accelerations in three directions. The equations for the acceleration response of the body are formulated as complex transfer functions multiplied by input accelerations from the three axes in the form of a frequency response function. Body behavior when exposed to random acceleration inputs measured at the floor of the railway vehicle is investigated across a frequency domain. Root Mean Square (RMS) values of the acceleration magnitudes in the body regions are calculated from the power spectral density (PSD) values of the acceleration responses. The absolute magnitude of the accelerations of the body is compared with the ride index, which is calculated using the input accelerations and standard methods. It is shown that the absolute magnitudes in the body regions are proportional to the standard ride index and that the ride index accurately reflects vibration damage to the body. A proposed seat design using the vibration magnitudes calculated with the human biodynamic model also is presented.