Ultrasound examination performed on a 36-year-old woman at 33 weeks of gestation showed the presence of isolated and bilateral ventriculomegaly in the fetus. Array-based comparative genomic hybridization (array-CGH) performed on uncultured amniocytes at 35 weeks of gestation revealed a 17q21.31 microdeletion. After genetic counseling, the pregnancy was terminated at 37 weeks of gestation. At autopsy, the fetus displayed facial dysmorphic features and triventricular ventriculomegaly. To our knowledge, this is the first case of a 17q21.31 microdeletion detected prenatally. Our report suggests that array-CGH should be performed when severe ventriculomegaly is observed in prenatal ultrasound examination.