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Intestinal diffuse ganglioneuromatosis is a rare, benign, neoplastic condition characterized by disseminated proliferation of neural elements. It has an established association with several systemic disorders including: multiple endocrine neoplasia IIB (MEN IIB) and von Recklinghausen’s disease. However, isolated GNs are very rare and sporadic. We report a case of a 6-year-old patient was referred to the emergency department due to a colon perforation during endoscopy. He then underwent sigmoidectomy and the pathologic studies revealed prominent signs of diffuse ganglioneuromatosis. Unfortunately, the patient died the day after because of the late diagnosis and treatment. Such presentation emphasizes the importance of considering diffuse ganglioneuromatosis, among other causes, in patients with intractable GI symptoms despite medical treatment.