The Wilms' tumor (WT) suppressor gene, WT1, is mutated in a small set of WTs and is essential for proper development of the urogenital system. The gene has three sites of transcriptional initiation and produces mRNA transcripts containing 5'-untranslated regions of more than 350 nucleotides. The mRNA, through two alternative splicing events, is predicted to direct the synthesis of four protein isoforms with molecular masses of 47-49 kDa. In this report, we identify and characterize novel WT1 protein isoforms having predicted molecular masses of 54-56 kDa. Mutational analysis of the murine wt1 mRNA demonstrates that the novel isoforms are the result of translation initiation at a CUG codon 204 bases upstream of and in frame with the initiator AUG. We show that these isoforms are present in both normal murine tissue and in WTs. Like WT1, the larger isoforms localize to the cell nucleus and are capable of mediating transcriptional repression. Our results indicate that regulation of WT1 gene expression is more complex than previously suspected and have important implications for normal and abnormal urogenital system development.