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Cornelia de Lange Syndrome (CdLS) is a rare congenital genetic disease causing abnormal unique facial phenotypes, several defects in organs and body parts, and mental disorder or intellectual disorder traits. Main causes of CdLS have been reported as variants in cohesin complex genes, in which mutations in the <i>NIPBL</i> gene have been estimated to account for up to 80%. Our study included three Vietnamese patients with typical CdLS phenotypes. Whole exome sequencing revealed two known heterozygous mutations c.6697G&gt;A (p.Val2233Met) and c.2602C&gt;T (p.Arg868X), and a novel heterozygous mutation c.4504delG (p.Val1502fsX87) in the <i>NIPBL</i> gene of the three patients. In silico analyses of the identified mutations predicted possible damaging and truncating effects on the NIPBL protein. Inherited analyses in the patients&#8217; families showed that all of the mutations are de novo. Our results lead a definitive diagnosis of patients with CdLS and expand the spectrum of mutations in the <i>NIPBL</i> gene. These findings also confirm whole exome sequencing is an efficient tool for genetic screening of CdLS.