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Branchio‐oto‐renal syndrome is characterized by branchial defects, hearing loss, preauricular pits, and renal anomalies. Mutations in EYA1are the most common cause of branchio‐oto‐renal and branchio‐otic syndromes. Large chromosomal aberrations of 8q13, including complex rearrangements occur in about 20% of these individuals. However, submicroscopic deletions and the molecular characterization of genomic rearrangements involving the EYA1gene have rarely been reported. Using the array‐comparative genomic hybridization, we identified non‐recurrent genomic deletions including the EYA1gene in three patients with branchio‐oto‐renal syndrome, short stature, and developmental delay. One of these deletions was mediated by two human endogenous retroviral sequence blocks, analogous to the AZFa microdeletion on Yq11, responsible for male infertility. This report describes the expanded phenotype of individuals, resulting from contiguous gene deletion involving the EYA1gene and provides a molecular description of the genomic rearrangements involving this gene in branchio‐oto‐renal syndrome. © 2010 Wiley‐Liss, Inc.