This article proposes a new framework for the inclusion of site effects in empirical ground-motion prediction equations (GMPEs) by characterizing stations through their one-quarter wavelength velocities and assessed confidence limits. The approach is demonstrated for 14 stations of the French accelerometric network (Réseau Accélérométrique Permanent). This method can make use of all the available information about a given site, for example, the surface geology, the soil profile, standard penetration test measurements, near-surface velocity estimated from the topographic slope, depth to bedrock, and crustal structure. These data help to constrain the velocity profile down to a few kilometers. Based on a statistical study of 858 real profiles from three different regions (Japan, western North America, and France) physically realistic profiles are generated that comply with the information available for each site. In order to evaluate the confidence limits for the shear-wave velocity profiles and derived site amplifications for each station, a stochastic method is adopted: several thousand profiles are randomly generated based on parameters derived in the statistical study and the constraints available for each station. Then, the one-quarter wavelength assumption is used to estimate the amplification for each station. It is found that a good knowledge of near-surface attenuation (i.e., or Q) is mandatory for obtaining precise amplification estimates at high frequencies. Nevertheless, the proposed scheme highlights the important differences in the uncertainties of the site amplifications, depending on the information available for a given station. We suggest that these results could, therefore, be used when developing GMPEs by weighting records from each station depending on the variability in the computed one-quarter wavelength velocities. This approach relies on the assumption that local site effects are only one-dimensional, which is far from true, especially in sedimentary basins. However, most GMPEs only model one-dimensional site effects, so this is not an issue specific to this study. Finally, a way to improve this technique is to use earthquakes or noise recorded at the stations to further constrain the shear-wave velocity profiles and to consequently derive more accurate one-quarter wavelength velocities.