We introduce procedures to validate site response in sedimentary basins as predicted using ground motion simulations. These procedures aim to isolate contributions of site response to computed intensity measures relative to those from seismic source and path effects. In one of the validation procedures, simulated motions are analyzed in the same manner as earthquake recordings to derive non-ergodic site terms. This procedure compares the scaling with sediment isosurface depth of simulated versus empirical site terms (the latter having been derived in a separate study). A second validation procedure utilizes two sets of simulations, one that considers three-dimensional (3D) basin structure and a second that utilizes a one-dimensional (1D) representation of the crustal structure. Identical sources are used in both procedures, and after correcting for variable path effects, differences in ground motions are used to estimate site amplification in 3D basins. Such site responses are compared to those derived empirically to validate both the absolute levels and the depth scaling of site response from 3D simulations. We apply both procedures to southern California in a manner that is consistent between the simulated and empirical data (i.e. by using similar event locations and magnitudes). The results show that the 3D simulations overpredict the depth-scaling and absolute levels of site amplification in basins. However, overall patterns of site amplification with depth are similar, suggesting that future calibration may be able to remove observed biases.