A number of different disorders involving first and second branchial arch anomalies have been described as distinct entities, including Treacher-Collins-Franceschetti syndrome, Goldenhar syndrome, Nager syndrome and Miller syndrome. The significant phenotypic overlap between these disorders raises the issue of a common developmental origin. After the identification of mutations in TCOF1 as a general cause of the Treacher-Collins-Franceschetti syndrome, TCOF1 mutations were excluded in patients with unilateral signs of the Goldenhar syndrome spectrum. We also present two rare cases of bilateral Goldenhar syndrome and familial microtia with meatal atresia, respectively, in whom we also excluded TCOF1 mutations. Thus, genetic heterogeneity in different disorders of the first and second branchial arch development is supported.