The objective of this study is to evaluate effects of the presently available 3D velocity model of the Mississippi embayment structure on the amplification of seismic waves by using simulated finite-difference seismograms. Effects of both 2D and 3D embayment basement structures were considered. The 3D model included information of the near-surface velocities that were derived from the existing 1D velocity models. The 2D crustal model was taken from Catchings (1999), which extended from Saint Louis, Missouri, to Memphis, Tennessee. Finite-difference seismograms were simulated for point sources embedded at both ends of the 2D structure. These seismograms were examined to distinguish features like peak amplitude amplifications and duration of seismograms when the seismic waves propagated from the Mississippi Embayment toward the Illinois basin and vice versa. To establish a working 3D structure model of the embayment, we compiled geologic information of the region on material properties of the shallow structure and used the 3D model developed at the Center of Earthquake Research Institute (ceri), Memphis, as the starting model. The 3D model was used to generate finite-difference seismograms along several profiles for a Mw 7.2 scenario earthquake occurring on the New Madrid fault zone. An equivalent 1D model, which included the basin materials, was also used to compare the 3D versus equivalent 1D ground motions simulated using the finite-difference method. To establish the amplification factors due to the surface sediments in the 3D model, finite-difference seismograms were also computed for a 1D hard-rock reference model. These 1D and 3D responses of the Mississippi embayment were used for estimating ground-motion amplification at sites where the depth to the basement is deeper than 500 m. Our investigation suggests that the deep structure of the Mississippi Embayment has little impact on long-period ground- motion amplitudes (T ≥ 2 sec) for large earthquakes that rupture in the central part of the basin. This supports the hypothesis that for engineering purposes ground motions simulated based on the equivalent 1D crustal model are adequate for representing ground motions from future large earthquakes (Mw > 7) occurring in the New Madrid seismic zone.