A Tunisian infant of consanguineous parents had pigmentary disorders, congenital deafness and long-segment Hirschsprung disease. Her elder sister had the same disorders but with short-segment aganglionosis. Their father, mother and two brothers are healthy without history of deafness, constipation or pigmentary disorder. We confirm that this Waardenburg-Hirschsprung association seems to be a distinct clinical entity with a possible autosomal recessive mode of inheritance. Linkage analyses performed in this family support the view that neither the RET locus (candidate for familial dominant Hirschsprung disease) nor the HuP2 locus (candidate for Waardenburg syndrome type I) are involved in the disease phenotype. We suggest that Waardenburg-Hirschsprung complex is a distinct genetic entity and at least one additional locus altering cranial neural crest cell development is responsible for pleiotropic features observed in this association.