Waardenburg syndrome is an autosomal dominant disorder characterised by sensorineural hearing loss, pigmentary abnormalities of iris, hair and skin and dystopia canthorum. The expression of clinical findings of Waardenburg syndrome is extremely variable. The potential sources of this variability include allelic variation, genetic heterogeneity, epistatic modifying genes and stochastic effects. This type of multifactorial inheritance based on oligogenic epistasis is very different from the model based on polygenic inheritance. Indeed in the first model, knowledge of the genotype at relevant modifier loci may allow prediction and possibly treatment of clinically relevant aspects of the phenotype. Therefore a more complete understanding of gene expression in Waardenburg could provide insights that are relevant to many other multifactorial diseases.