We report a novel mutation in WT1 exon 9 (1214 A>G) resulting in an amino acid change from H to R at codon 405 in a 46 XY female patient who had congenital hypertrophic pyloric stenosis, pseudohermaphroditism masculinus, renal failure, and Wilms tumor, and died at the age of 22 months. The patient demonstrated the difficulty in diagnosing a patient with intersex before conclusive genetic characterization.