The effects of the short-wavelength heterogeneity of the crustal structure on predicted ground motion at periods of 1 s and longer were investigated by conducting three-dimensional finite-difference simulations using a detailed realistic velocity model of the Kanto region of Japan. The short-wavelength heterogeneity of the media within the upper crust was randomly modeled using the exponential-type autocorrelation function where the velocity standard deviation was set to 5%. Combinations of heterogeneous media with various correlation lengths and point source models with various depths and durations were considered in order to investigate the variability of the predicted ground motion and the sensitivity to the parameters. The effects of random heterogeneity on the simulated ground motion appeared as a result of changes in the amplitude and phase of both the direct waves and later phases, as well as the spectral peaks of the response spectra. Ground-motion variability, in terms of peak ground velocity (PGV) and velocity response spectra (Sv), was evaluated using the residual, or the difference in logarithm of PGV and Sv between the ground motion computed with and without random heterogeneity. While the residual averaged over the surface of the computed area was almost negligible in the studied period range, the variability of the residual was found to increase with distance and to be larger for point sources with shorter durations. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.