AbstractBackgroundCongenital hydrocephalus is one of the symptoms of Walker–Warburg syndrome that is attributed to the disruptions of the genes, among which the B3GALNT2 gene is rarely reported. A diagnosis of the Walker–Warburg syndrome depends on the clinical manifestations and the whole‐exome sequencing after birth, which is unfavorable for an early diagnosis.MethodsWalker–Warburg Syndrome was suspected in two families with severe fetal congenital hydrocephalus. Whole‐exome sequencing and Sanger sequencing were performed on the affected fetuses.ResultsThe compound heterozygous variants c.1A>G p.(Met1Val) and c.1151+1G>A, and c.1068dupT p.(D357*) and c.1052 T>A p.(L351*) in the B3GALNT2 gene were identified, which were predicted to be pathogenic and likely pathogenic, respectively. Walker–Warburg syndrome was prenatally diagnosed on the basis of fetal imaging and whole‐exome sequencing.ConclusionsOur findings expand the spectrum of pathogenic mutations in Walker–Warburg syndrome and provide new insights into the prenatal diagnosis of the disease.