X-ray topography is a powerful method for analyzing crystal defects and strain in crystalline materials non-destructively. However, conventional X-ray topography uses simple X-ray diffraction images, which means depth information on defects and dislocations cannot be obtained. We have therefor developed a novel three-dimensional micro-X-ray topography technique (3D μ-XRT) that combines Bragg-case section topography with focused sheet-shaped X-rays. The depth resolution of the 3D μ-XRT depends mainly on the focused X-ray beam size and enables non-destructive observation of internal defects and dislocations with an accuracy on the order of 1 μm. The demonstrative observation of SiC power device chips showed that stacking faults, threading screw, threading edge, and basal plane dislocations were clearly visualized three-dimensionally with a depth accuracy of 1.3 μm. 3D μ-XRT is a promising new approach for highly sensitive and non-destructive analysis of material crystallinity in a three-dimensional manner.