In a family with X-linked ichthyosis (XLI), non-invasive prenatal testing (NIPT) of a pregnant woman revealed a deletion of approximately 2 Mb at Xp22.31. This deletion was confirmed by chromosome microarray analysis and involves the steroid sulfatase gene (STS), which is responsible for XLI. Clinical signs of XLI were also found in other family members. XLI is a recessive inherited skin disease characterized by dark brown polygonal scales. The clinical manifestations of XLI are not obvious, which makes genetic diagnosis of patients difficult. Incidental findings from NIPT show that copy number variations (CNVs) can help predict pathogenic CNVs both in the fetus and in the whole family genome. In prenatal screening, we should pay more attention to CNVs identified by NIPT.