To investigate genetic etiology of Dandy-Walker syndrome with array-based comparative genomic hybridization (array-CGH).Eight fetuses with Dandy-Walker malformations but normal karyotypes by conventional cytogenetic technique were selected. DNA samples were extracted and hybridized with Affymetrix cytogenetic 2.7 M arrays by following the manufacturer's standard protocol. The data were analyzed by special software packages.By using array-CGH technique, common deletions and duplication on chromosome 7p21.3 were identified in three cases, within which were central nervous system disease associated genes NDUFA4 and PHF14.Copy number variations (CNVs) of chromosome 7p21.3 region are associated with Dandy-Walker malformations which may be due to haploinsufficiency or overexpression of NDUFA4 and PHF14 genes.