This work focuses on the effects of the spatial variability of the seismic motion due to site effects on the seismic response of multi-span viaducts on pile foundations. A methodology is proposed to include the effects of both soil-structure interaction and non-synchronous seismic actions in the nonlinear response of bridges. Then, some results of nonlinear dynamic analyses performed on a multi-span bridge founded on soft soil are presented. The deposit is characterized by an inclined layout of the bedrock and the seismic input is represented by a set of suitably selected real accelerograms. Comparisons with results obtained considering synchronous seismic motions demonstrate the influence of site effects on the response of long bridges