The kidneys of 37 Japanese Black calves aged 2 to 65 months diagnosed with Claudin 16 (CL-16) defect by the DNA-based test were examined pathologically. The animals exhibited clinical symptoms such as growth impairment, renal failure, overgrowth of hooves, and anemia at a young age. There was no correlation between the time of onset and age. Kidney weights relative to body weight were similar to those in normal animals, but both kidney net weights and size were reduced due to atrophy in animals that showed severe renal dysfunction. Histopathological examination of the kidneys showed reduction in the number of glomeruli, compensatory hypertrophy of glomeruli and tubules, and glomerular and tubular atrophy accompanied by interstitial fibrosis and lymphocytic infiltration. Glomeruli were clearly less in number in the kidneys of CL-16-defective animals than those of normal animals even in the cases with mild lesions. A small number of immature glomeruli and tubules were also detected, suggesting that there were fewer nephrons developed at birth in CL-16-defective animals. It was suggested that a defect of the CL-16 gene is involved in the "abnormal development of nephrons". Immunohistopathological examination of the kidneys showed that the epithelium of thick ascending limb of Henle was stained with anti-CL-16 antibody in the control animals, but not in the affected animals, suggesting a defect of CL-16 in the epithelium of renal tubules in the affected animals.