The VACTERL association refers to anomalies of the vertebral anomalies, anal atresia, cardiovascular malformations, tracheo-esophageal fistula with esophageal atresia (TEF-EA), renal anomalies, and/or limb-anomalies. Although a few genetic disorders overlapping with these anomalies have been known, genetics for the VACTERL association is not well described. We performed array CGH analysis to identify DNA copy number changes in patients with full or partial VACTERL association. Six patients with two or more components of the VACTERL association and apparently normal karyotype were investigated by high-resolution whole genome array CGH. Two of them had DNA copy number aberrations which were deletion of 10 Mb at 6q25.3 and gain of 1 Mb at 8p11.21, respectively. A deletion of 6q25.3-qter is one of the common terminal deletion syndromes and contains more than 40 genes in this case. A gain of 1 Mb in 8p11.21 encompasses 7 genes, among which some genes are not included in CNV region. Both of patients didn’t manifest TEF-EA, but presented multiple non-VACTERL anomalies. These results show that DNA copy number aberration is not frequent in full or partial VACTERL association including TEF-EA. Array CGH enables us to detect genetic etiology for the cases of the VACTERL association with accompanying multiple non-VACTERL anomalies.