This comparison study between MPRAGE with GRAPPA and MPRAGE with Wave-CAIPI has been performed at the clinical MR scanner. MPRAGE with Wave-CAIPI 3×3 shows relatively good contrast despite its short scan time of 1 m 42 s. No segmentation error was found in MPRAGE with Wave-CAIPI 3×3 in our cohort. The correlation of cerebral cortex and cerebral white matter was very high between 2 MPRAGEs. In deep gray matters except pallidum and hippocampus, the correlation of VOIs were also high. These results suggest that volumes derived from automated segmentation of MPRAGE with Wave-CAIPI are reliable measures.