This study reports the identification of a 2.3-Mb de novo overlapping microdeletion on chromosome 8q12 in two individuals with CHARGE syndrome, a condition characterized by nonrandom congenital anomalies affecting multiple tissues. Sequence analysis of genes in this region identified mutations in the *CHD7* gene in 10 out of 17 individuals without microdeletions, suggesting that haploinsufficiency of *CHD7* could account for most cases of CHARGE syndrome. *CHD7* is a member of the chromodomain helicase DNA-binding (CHD) gene family, and its mutations include stop-codon and missense mutations, as well as a mutation at an intron-exon boundary. The study highlights the effectiveness of high-resolution genome-wide screening by array comparative genomic hybridization (array CGH) in identifying underlying genetic causes of sporadic malformation syndromes.This study reports the identification of a 2.3-Mb de novo overlapping microdeletion on chromosome 8q12 in two individuals with CHARGE syndrome, a condition characterized by nonrandom congenital anomalies affecting multiple tissues. Sequence analysis of genes in this region identified mutations in the *CHD7* gene in 10 out of 17 individuals without microdeletions, suggesting that haploinsufficiency of *CHD7* could account for most cases of CHARGE syndrome. *CHD7* is a member of the chromodomain helicase DNA-binding (CHD) gene family, and its mutations include stop-codon and missense mutations, as well as a mutation at an intron-exon boundary. The study highlights the effectiveness of high-resolution genome-wide screening by array comparative genomic hybridization (array CGH) in identifying underlying genetic causes of sporadic malformation syndromes.