The authors report on a patient with Chiari I malformation associated to Waardenburg phenotype, multiple malformations, osteochondrodysplasia and microdeletion of 1q21,1 chromosome, of which they underline the rarity. The pathogenesis connected to the features of neural crest cells-derived structures with mesodermal-derived tissues, mainly in the facial and boundary region of malformed posterior cranial fossa, is discussed. The authors hypothesize that chromosomal microdeletion, acting directly or on contiguous gene(s) or by long range control of gene expression, have modified the function of some developmental genes, causing consequently the association of symptoms observed in the patient.