We presented the case of a neonate with portal venous gas and pulmonary gas embolism. The patient presented with severe respiratory distress and abdominal distension 12 hours after birth. An ultrasound revealed intravascular microbubbles moving into a pulmonary artery that were traveling from the portal venous system through a ductus venosus. Additional clinical observations were hypotension and a sudden decrease in end-tidal carbon dioxide with a markedly discrepant high Pco(2), indicating a massive pulmonary gas embolism. Operative findings revealed congenital ileal atresia and meconium peritonitis with abscess. Gas-forming Escherichia coli was recovered from the abscess contents. The patient had respiratory distress, shock, disseminated intravascular coagulation, and intractable diarrhea but eventually recovered and was discharged on the 131st postoperative day.