To explore the genetic basis for a fetus with Dandy-Walker malformation.G-banding chromosomal karotyping, single nucleotide polymorphism microarray (SNP array) and fluorescence in situ hybridization (FISH) were carried out for the fetus. Chromosomal karyotyping and FISH assay were also carried out for both parents.SNP array has detected a 4266 kb microdeletion at 6p25.3p25.1 in the fetus, which was confirmed by FISH. FISH analysis of the parents demonstrated that the father has carried a cryptic t(6;14) (p25.1;p13) translocation, while the fetus has a der(6)t(6;14)(p25.1;p13) derived the paternal translocation.The der(6)t(6;14)(p25.1;p13) probably underlies the Dandy-Walker malformation in the fetus. The 6p25.3p25.1 microdeletion is due to unbalanced gametes produced by the father's cryptic balanced translocation.