Guidelines for seismic spectral amplification are provided in current building codes based on soil strength/stiffness by means of seismic site class. However, current codes do not make a difference between fully saturated and unsaturated soil deposits and do not account for effects of soil heterogeneity on seismic amplification. This study investigates the effect of natural small scale soil heterogeneity and degree of saturation on spectral amplification by means of transient nonlinear finite element analyses. Only cohesionless soil (sand) is considered in this study. The effects of presence of a structure are also studied for soils with two different relative densities. The analysis results are compared with guidelines in the Canadian Building Code and results from the literature. Design recommendation and guidelines on spectral amplification of seismic ground motion are provided in terms of the short (0.2s) and long period (1.0s) amplification factor.