Scientists have identified and located four different genes for Waardenburg syndrome: PAX3, MITF, EDNRB, and EDN3. WS type 1 and 3 have been associated with mutations in the PAX3 gene; WS type 2 with the MITF gene; and WS type 4 with the EDNRB and EDN3 genes. While scientists are studying all of these genes, currently, the most information is available on the PAX3 and MITF genes and their role in Waardenburg syndrome.

The PAX3 gene is located on chromosome 2 and controls some aspects of the development of the face and inner ear. The MITF gene is found on chromosome 3. It also controls the development of the ear and hearing. Scientists are now studying these genes to better understand how they operate in controlling the normal growth of the ear and the development of hearing. This information will help scientists understand why persons with WS sometimes develop hearing problems.