Ventricular septal defect (VSD) is the most common form of congenital cardiovascular malformation and an important contributor to the substantially increased morbidity and mortality in infants. Emerging evidence indicates the genetic basis for the pathogenesis of congenital VSD in a significant proportion of patients. However, congenital VSD is a genetically heterogeneous disease and the genetic defects responsible for VSD in the overwhelming majority of cases remain unclear. In this study, the entire coding region of the GATA6 gene, which encodes a zinc-finger transcription factor crucial to normal cardiogenesis, was sequenced in 130 unrelated patients with congenital VSD. The available relatives of the index patient carrying the identified mutation and 200 unrelated ethnically matched healthy individuals used as controls were subsequently genotyped. The functional characteristics of the mutant GATA6 were assessed in contrast to its wild-type counterpart using a luciferase reporter assay system. As a result, a novel heterozygous missense GATA6 mutation, p.G220S, was identified in a proband with VSD. The variation was absent in 400 control chromosomes and the altered amino acid was highly conserved evolutionarily across species. Genetic analysis of the family members of the mutation carrier showed that the substitution co-segregated with VSD was inherited as an autosomal dominant trait. Functional analysis demonstrated that the p.G220S mutation of GATA6 was associated with significantly decreased transcriptional activity. The findings provide novel insight into the molecular mechanism involved in VSD, implying the potential clinical implications in the gene-specific prophylaxis and therapy of this common developmental abnormality in neonates.