We report a boy who presented at 3 years with nephrotic syndrome and end-stage renal failure. Although histopathological findings showed end-stage kidney, isolated diffuse mesangial sclerosis (IDMS) was suspected because of his clinical course, and was confirmed by the presence of WT1 (Wilms tumor suppressor gene) mutation. He did not have ambiguous genitalia or Wilms tumor. The karyotype was 46:XY. A constitutional mutation in exon 7 (953G-->A, 312Arg-->Gin) was detected. A few cases of male IDMS, associated with WT1 mutations, have been reported. We believe that investigation for the WT1 mutation should be performed not only in Denys-Drash syndrome and IDMS, but also in end-stage renal disease with unexplained nephrotic syndrome of early onset. WT1 mutation-associated nephrotic syndrome has an increased risk of Wilms tumor. Careful ultrasound evaluations or bilateral nephrectomies are indicated.