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Gastrointestinal duplication cysts are rare congenital malformations, with esophageal and gastric duplication cysts being among the rarest. We report an 8-week-old female who presented to the emergency department with failure to thrive and was subsequently found to have multiple gastric and esophageal duplication cysts that had ruptured intrathoracically and intra-abdominally. We describe the diagnosis and management of this patient who underwent successful resection of 4 gastrointestinal duplication cysts. This report emphasizes the unexpected, and sometimes relatively benign, presentations of gastrointestinal duplication cysts. To our knowledge, this is the first reported occurrence of multiple duplication cysts that independently ruptured thoracically and abdominally.