Weak-motion geotechnical array recordings at 38 stations of the Japanese strong-motion network KiK-Net from the 2003 Mw 7.0 Miyagi-Oki aftershock sequence are used here to quantify the amplification and attenuation effects of near-surface formations to incident seismic motion. Initially, a seismic waveform optimization algorithm is implemented for the evaluation of high-resolution, low-strain velocity (Vs), attenuation (Qs), and density (ρ) profiles at the sites of interest. Based on the inversion results, Vs versus Qs correlations are developed, and scattering versus intrinsic attenuation effects are accounted for in their physical interpretation. Surface-to-downhole traditional spectral ratios (SSR), cross-spectral ratios (c-SSR), and horizontal-to-vertical (H/V) site-response estimates are next evaluated and compared, while their effectiveness is assessed as a function of the site conditions classified on the basis of the weighted average Vs of the upper 30 m (Vs30) of the formations. Single and reference-station site-response estimates are successively compared to surface-to-rock outcrop amplification spectra and are evaluated by deconvolution of the downhole records based on the inversion results; comparison of the observed SSR and estimated surface-to-rock outcrop amplification spectra illustrates the effects of destructive interference of downgoing waves at the downhole instrument level as a function of the site class. Site amplification factors are successively computed in reference to the National Earthquake Hazards Reduction Program (NEHRP) B–C boundary site conditions (Vs30=760 m/sec), and results are compared to published values developed on the basis of strong-motion data and site-response analyses. Finally, weak-motion SSR estimates are compared to the mainshock spectra, and conclusions are drawn for the implications of soil nonlinearity in the near surface. Results presented in this article suggest that currently employed site classification criteria need to be reevaluated to ensure intraclass consistency in the assessment of amplification potentials and nonlinearity susceptibility of near-surficial soil formations.