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Metabolic acidosis is often encountered in a sick neonate and intestinal duplication with heterotopic gastric mucosa is a well-established condition.  We present a previously unreported relationship between neonatal metabolic acidosis, resulting from transperitoneal absorption of hydrochloric acid, and a ruptured non- communicating ileal duplication cyst with gastric mucosal heterotopia. The neonate recovered rapidly after resection of the ileal duplication. We present this case to highlight a rare but surgically correctable cause of neonatal metabolic acidosis.