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Introduction: Postoperative complications of stomas in necrotizing enterocolitis (NEC) typically affect the proximal limb. Complications of the distal limb are rarely reported. Case presentation: A 17-day-old newborn underwent an end ileostomy and an ileal Hartmann's pouch due to necrotizing enterocolitis (NEC). Eight weeks after the surgery, he passed bloody stool through the anus. No drop in his hemoglobin level was observed. He was made NPO, and no further bloody stool was seen after 24 hours. Ten weeks post-surgery he developed acute vomiting, and a 10-cm segment of bowel was seen prolapsed through the anus. The end of the prolapsed bowel was blind, raising the suspicion of a complete prolapse of the ileal Hartmann's pouch. He was taken to the operating room for an exploratory laparotomy. We found that the ileal Hartmann's pouch had intussuscepted into the ileocecal valve, progressed through the colon and the rectum, and prolapsed through the anus. We reduced the bowel manually. The involved ileum and colon were markedly swollen, and partially necrotic. The necrotic segments were resected, and the ileostomy was reversed. The patient was discharged one month later and had no adverse complications at two months of follow up. Conclusion: Although rare, intussusception of an ileal Hartmann's pouch should be ruled out in patients that have a Hartmann's pouch and develop vomiting and bloody stool.