To clarify the pathogenesis of total intestinal aganglionosis, an extremely severe from of neural crest-derived cell migration disorder of the gut, the authors studied possible germline mutations of the RET proto-oncogene (10q11.2) in five pedigrees at high risk for congenital aganglionosis. All five patients analyzed were boys, and one had a family history of Hirschsprung's disease. Genomic DNA was extracted from lymphoblastoid cell lines established from patients and their relatives. Polymerase chain reaction (PCR) products, which were amplified using specific primers (RET; exon 1 approximately 20), were electrophoresed to analyze the single-strand conformational polymorphism (SSCP) patterns. DNA sequences were determined in pedigrees showing abnormal SSCP bands. Among the five patients, three germline mutations were found in the receptor tyrosine kinase domain (exon 15; codons 884, 897, and 904). Amino acid substitutions of the Ret protein were predicted based on the mutated nucleotide changes. Phenotypic variations of congenital aganglionosis may depend on the RET mutation pattern and other genetic or environmental determinants. In our series of patients, male sexuality and germline mutation of the RET tyrosine kinase domain were the most likely factors contributing to this form of Hirschsprung's disease.