Van der Woude syndrome (VWS) (OMIM 119300) is a dominantly inherited developmental disorder that is characterized by pits and/or sinuses of the lower lip and cleft lip and/or cleft palate. Mutations in the interferon regulatory factor 6 gene (IRF6) have been recently identified in patients with VWS, with more than 60 mutations reported. We report the phenotypic variants of the syndrome in a family and present the application of the multicolor chromosome banding (mBAND) analysis in the identification of complex intrachromosome rearrangements of chromosome 9 in a child with VWS. The authors conclude that increased heterochromatin on chromosome 9 did not have any effect on the phenotypic expression of the syndrome in the family that was studied.