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Introduction Vitamin B12 deficiency can result in macrocytic anemia. Neurologic abnormalities of B12 deficiency include sensory deficits, loss of deep tendon reflexes, movement disorders, neuropsychiatric changes and seizures. Segmental involvement of the distal ileum, such as in tuberculosis, can cause vitamin B12 deficiency. To our knowledge, macrocytic anemia with unusual manifestations such as brain atrophy and seizures due to intestinal tuberculosis has not been reported in the literature. Case presentation A 14-year-old girl presented with complaints of paraplegia, ataxia, fever and fatigue that had started a few months earlier and which had been getting worse in the last three weeks. Her laboratory results were indicative of macrocytic anemia with a serum B12 level Conclusion Vitamin B12 deficiency should be considered in patients with neurologic features such as paresthesia, sensory deficits, urinary incontinence, dysarthria, and ataxia. The underlying cause of B12 deficiency should be determined and treated to obviate the patients' need for long term vitamin B12 therapy.