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A male neonate was clinically diagnosed with congenital intestinal atresia. Surgical operation was performed and the ileum including the atretic portion was resected. Grossly, there was a plaque-like elevation of mucosa at the proximal side of the ileal atresia. Microscopic examination of this lesion revealed proliferation of severely atypical glands. Although dysplasia was a serious diagnostic concern, we concluded that ischemia due to the intestinal atresia induced this benign pseudodysplastic regenerative mucosa, judging from the pattern of coexisting inflammation and the literature review.