A 27-year-old woman with short stature, sensorineural deafness, and renal dysfunction was hospitalized for evaluation. The serum lactate and pyruvate concentrations were elevated. The analysis of her mitochondrial DNA revealed an A-to-G mutation of the tRNA(Leu (UUR)) gene at the 3243 position. Renal biopsy revealed many sclerotic glomeruli, advanced tubulointerstitial changes, and numerous swollen mitochondria of the tubular cells. It was concluded that the patient's mitochondrial gene mutation was etiologically related to her nephropathy. The clinicopathologic features of this patient, as contrasted to the previous reports, suggested that renal involvement due to this mitochondrial gene mutation can be heterogeneous.