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The association between epidermolysis bullosa and congenital pyloric atresia is rare, but is a known distinct clinical entity with autosomal recessive inheritance. We report on a case of a baby girl born by cesarean section at 37 weeks’ gestation to a G7 P7 mother and weighed 2.84 kg. At birth, there was denuded skin over the right leg from the knee joint up to the middle of the right foot. Abdominal radiograph was thus performed and indicated absent gas in the small bowel and single bubble appearance of the stomach. Pyloric atresia was surgically corrected. Electron microscopy of skin biopsies showed junctional epidermolysis bullosa. There was typical nail dystrophy and no corneal lesions; ultrasonography for the renal system was normal. At 4 months of age, the baby required gastrostomy and fundoplication for severe failure to thrive. Six weeks after her second surgical procedure, the patient presented to the emergency room dead; the parents provided a typical scenario of sudden infant death syndrome at home. Examination indicated no signs of child abuse; the parents refused an autopsy exam for the child.