One of the critical aspects of the geotechnical earthquake engineering is to evaluate the response of soil grounds under earthquake loading. Generally, three types of uncertainties are contributed to the seismic site response analysis — ground motion variability, site property variability and uncertainty associated with the constitutive soil models and numerical methods used for the analysis. This study focuses on quantifying the effects of ground motion variability and site property variability on the seismic ground response analysis. An equivalent-linear approach and a modified version considering frequency-dependent modulus and damping are used to perform the seismic site response analysis. Two types of intrinsic variability in ground motion intensity measures are considered in the site response analysis. The first type is the variability from a scenario earthquake, given the earthquake magnitude, rupture distance etc, and is termed as “unconditional” variability. The second type is the variability of the ground motion intensity measures conditioned on a specified response spectrum value at a specified spectral period, which is termed as “conditional” variability. In this study, a new ground motion selection scheme is implemented to select ground motions that preserve the conditional and unconditional variability of the spectral acceleration (Sa). Due to the complexity of ground motion time histories, different ground motion intensity measures can only represent certain aspects of ground motion characteristics. Thus the ground motion selection scheme is further extended to simultaneously capture the joint unconditional and conditional variability of multiple intensity measures, specifically the spectral accelerations and cumulative absolute velocity (CAV). Soil property variability is also an important source of uncertainties in seismic ground analysis since soil properties vary spatially across the site and variations in soil properties can change the surface response considerably. Two statistical models ...