A 38-year-old man with mild sensorineural hearing loss, diabetes mellitus, proteinuria, and slight renal dysfunction was admitted to our hospital for a renal biopsy to determine the cause of kidney disease. His elder sister and mother also had sensorineural hearing loss and renal failure, suggesting the existence of a common genetic disease in this family. Although the clinical features of the patient were similar to features of Alport syndrome, renal biopsy revealed no sign of Alport syndrome. We next considered a possibility of a mitochondrial kidney disease described by Jansen in 1997. Indeed, genetic analysis of mitochondrial DNA clarified the existence of A3243G mutation in the patient and his sister. This syndrome should be recognized by nephrologists as a differential diagnosis of Alport syndrome, diabetic nephropathy, and primary glomerular diseases.