Response spectra of earthquake ground motions are important in the earthquake-resistant design and reliability analysis of structures. The formulation of the response spectrum in the frequency domain efficiently computes and evaluates the stochastic response spectrum. The frequency information of the excitation can be described using different functional forms. The shapes of the calculated response spectra of the excitation show strong magnitude and site dependency, but weak distance dependency. In this paper, to compare the effect of the earthquake ground motion variables, the contribution of these sources of variability to the response spectrum’s uncertainty is calculated by using a stochastic analysis. The analytical results show that earthquake source factors and soil condition variables are the main sources of uncertainty in the response spectra, while path variables, such as distance, anelastic attenuation and upper crust attenuation, have relatively little effect. The presented formulation of dynamic structural response in frequency domain based only on the frequency information of the excitation can provide an important basis for the structural analysis in some location that lacks strong motion records.