A family with a case of two times of fetal hydrocephalus pregnancies was reported.The genetic etiology was analyzed by single nucleotide polymorphism array(SNP array)and whole-exome sequencing(WES).No pathogenic and likely pathogenic copy number variants were found from SNP array.The fetal was found to harbor a likely pathogenic c.287A>G mutation in exon 2 of POMT2 gene from the father and a pathogenic c.1362G>A mutation in exon 13 of POMT2 gene from the mother.The fetal carried the compound heterozygous mutations of POMT2 gene and so was diagnosed with Walker-Warburg syndrome(WWS).For a family with recurrent fetal hydrocephalus while excluding pathogenic and likely pathogenic copy number variants of fetal chromosome,WES is available with a view to identify the genetic etiology and to provid genetic data for reproduction.