Objective?To perform the genetic analysis for a fetus with Dandy-Walker syndrome and congenital heart disease revealed by ultrasonography.?Methods?The skin samples of induced labor fetus were analyzed by single nucleotide polymorphism array (SNP array) and verified by multiplex ligation-dependent probe amplification (MLPA). The peripheral blood samples of fetal parents were analyzed by fluorescence in situ hybridization (FISH).?Results?SNP array showed that the fetus carried a 5.4 Mb microdeletion at 6p25.3p25.1 and a 4.2 Mb microduplication at Xq28, which were pathogenic copy number variations. The verification results of MLPA were consistent with those of SNP array. FISH analysis of the peripheral blood samples from fetal parents showed no abnormalities such as deletion, duplication or translocation.?Conclusion?The microdeletion of 6p25.3p25.1 and microduplication of Xq28 in the fetus are new mutations, which may be related to Dandy-Walker syndrome and congenital heart disease indicated by ultrasonography.