This paper is devoted to investigate the effects of near-fault ground motions on the seismic responses of nonlinear MDOF structures considering soil-structure interaction (SSI). Attempts are made to take into account the effects of different frequency-content components of near-fault records including pulse-type (PT) and high-frequency (HF) components via adopting an ensemble of 54 near-fault ground motions. A deep sensitivity analysis is implemented based on the main parameters of the soil-structure system. The soil is simulated based on the Cone model concept, and the superstructure is idealized as a nonlinear shear building. The results elucidate that SSI has approximately increasing and mitigating effects on structural responses to the PT and HF components, respectively. Also, a threshold period exists above which the HF component governs the structural responses. As the fundamental period of the structure becomes shorter and structural target ductility reduces, the contribution of the HF component to the structural responses increases, elaborately. Soil flexibility makes the threshold period increase, and the effect of the PT component becomes more significant than the HF one. In the case of soil-structure system, slenderizing the structure also increases this threshold period and causes the PT component to be dominant. Copyright © 2013 John Wiley & Sons, Ltd.