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Enteric duplication cysts are an uncommon congenital anomaly that can occur anywhere along the gastrointestinal tract. These rare abnormalities are predominantly diagnosed in children and seldom reported in adults. We report a case of a male in his 50s who presented with an acute abdomen due to perforation peritonitis. Emergency exploratory laparotomy revealed two communicating jejunal duplication cysts, one of which was perforated. The involved jejunal segment was resected, and a primary end-to-end anastomosis was performed. Ultrasonography, CT and MRI can assist in making a preoperative diagnosis; however, intraoperative diagnosis is common and histological examination is required for confirmation. In this case, the congenital anomaly was identified intraoperatively and managed surgically. Increased awareness of this rare congenital entity among clinicians can aid in early recognition and appropriate surgical planning.