Congenital aganglionosis rat (AR) is a mutant with an autosomal recessive gene (sl), which shows megacolon caused by the absence of myenteric ganglion cells and white coat-color with a small pigmented spot on the head. Recently, targeted disruption of the endothelin-B (ETB) receptor gene (EDNRB) in the mouse has been reported to cause aganglionic megacolon and coat color spotting resembling the phenotypes of the sl/sl rats. To identify the mutation responsible for the phenotypes of the sl/sl rats, we determined the nucleotide sequences of the EDNRB genes of the sl/sl rats and found that a 301-bp region intervening between direct repeat sequences was deleted in the EDNRB gene, and the deletion produces various transcripts due to aberrant splicing.