In this work we report on the development of a novel technique for fat-saturated three-dimensional (3D) diffusion-weighted (DW) MRI sequence based upon 3D magnetization-prepared rapid gradient-echo (3D-MP-RAGE). In order to saturate fat, two kinds of procedures were competed CHESS-DW-3D-MP-RAGE sequence (CHESS-3D-DWI) and DW-3D-MP-WE-RAGE sequence (WE-3D-DWI) "chemical shift selective: CHESS method vs. water-excitation: WE method". The CHESS-3D-DWI sequence and WE-3D-DWI sequence were compared in terms of their degree of fat suppression. In CHESS-3D-DWI sequence a preparation phase with a "CHESS-90 degrees RF-motion probing gradient: MPG-180 degrees RF-MPG-90 degrees RF" pulse-train was used to sensitize the magnetization to fat-saturated diffusion. In contrast, WE-3D-DWI sequence a RAGE-excitation pulse with a "binominal-pulse 1-1 or 1-2-1" was selected to water-excited (fat-saturated) diffusion imaging. These imaging were done during in vivo studies using an animal experiment. From experimental results obtained with a phantom, the effect of diffusion weighting and the effect of fat-saturation were confirmed. Fat-saturation was much better in the WE-3D-DWI sequence than CHESS-3D-DWI sequence. From rat experimental results, fat-saturated diffusion-weighted image data were obtained. This sequence was useful for in vivo imaging.