Presented here is an analysis of the effects of soil-foundation-structure interaction (SFSI) on seismic response of highway bridges. Of particular importance is the issue of input motions, their scaling and application to the SFS models. The analysis presented in this paper addresses the influence of inelastic behavior of both the soil and the structural components during seismic response evaluation of highway bridge systems. At the system level, the additional flexibility introduced by the soil-foundation system results in increased displacement demands under moderate to severe ground motions. Additionally, it is also demonstrated that that SFS interaction can sometimes have a beneficial effect on the superstructure response and sometimes produce detrimental effects on the system behavior and is dependent on the characteristics of the earthquake motion. It is shown that each SFS intearacton problem has to be analyzed fully and that it is almost impossible to draw general conclusions about the behavior of the SFS system during seismic motions.