Pyloric atresia-junctional epidermolysis bullosa syndrome (PA-JEB) is an autosomal recessive inherited rare blistering disorder caused by mutations in ITGA6 or ITGB4, genes encoding integrin alpha6 or beta4, respectively. In this study, we have disclosed the mutations in ITGB4 in a Korean patient with PA-JEB. The proband, who showed skin blisters, was diagnosed as having pyloric atresia and died 2 years after birth. Mutational analysis showed a novel 594insC maternal mutation in exon 7, which led to premature termination codon (PTC), and a novel Q425P paternal mutation in exon 11. Q425P mutation was not detected in 200 alleles obtained from a normal healthy Korean control, and was shown to reduce alpha-helix forming ability in integrin beta4 a by Garnier alpha-helicity plot of the protein, indicating that this mutation is pathogenic but not polymorphism. The phenotype in the present case can be explained by (1) the combination of PTC and missense mutation, and (2) amino-acid substitution occurring for the amino acid not preserved in the integrin beta family. Our results contribute to further the accumulation of mutation data for better understanding of the genotype/phenotype correlation in PA-JEB, and may give profound insight into the role of integrins alpha6 and beta4.