X-ray crystal interferometer-based X-ray phase-contrast microtomography (phase-contrast microtomography) is able to image microstructures within soft tissue without the use of a contrast agent. Here we determined the feasibility of using this technique in the non-destructive inspection of formalin-fixed kidney tissue from certain hamsters that spontaneously develop mesangial thickening with focal and segmental glomerulosclerosis, and from age-matched Syrian hamsters. We used a triple Laue-case X-ray interferometer with a 40 microm-thick analyzer, a sample cell, and an X-ray charge-coupled-device camera with a 4.34 microm pixel size. Images of glomeruli and tubular structures were similar to those seen using 40-100 x magnification on an optical microscope. In samples from two female glomerulosclerotic hamsters, seven scattered lesions were detected. The wedge-shaped pathological lesions included mild atrophic tubular walls, markedly dilated tubular lumen, high-density glomeruli, and widening of Bowman's space. The microvasculature was distinctly visualized in the specimens without any contrast agents. Hence, phase-contrast microtomography can detect small scattered lesions in diseased kidney tissue and is a powerful auxiliary tool for pre-histological evaluations.