Objective　To evaluate the relationship between the number of copies of genes and congenital diaphragmatic hernia by the detection of multiple loci in infants with congenital diaphragmatic hernia. Methods　Multiple loci were analyzed by Microarray analysis of Affymetrix Cytoscan 750 k in 11 neonates with congenital diaphragmatic hernia, in whom 1 case was twins,and his fraternal twins were diagnosed of fetuse intestinal dilatation. Results　A homozygous deletion (8 p11.22 arr[hg19]) was found in one neonate with congenital diaphragmatic hernia, and was eventually confirmed that the depolymerization of the biotin and metalloprotease (ADAM) 3A genes lead to homozygous deletion of the 1~15 exon. Conclusion　The alteration of ADAM3A copy number may be the cause of congenital diaphragmatic hernia.