Branchio-oto-renal syndrome (BOR) is an autosomal dominant genetic disorder characterized by branchial fistulas, hearing impairment, renal malformations and auricular anomalies. Pathogenic mutations have been discovered in several genes such as EYA1, SIX5, and SIX1. However, it has a high penetrance with variable expressivity. The clinical and genetical heterogeneity is widespread amongst and within families. In this review, we describe the clinical manifestations and pathogenic genes with copy number variations in detail, and emphasize the criteria clinically and genetically to provide the basis for clinical diagnosis of BOR and genetic counseling.