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To examine the effect of allogeneic hematopoietic cell transplantation (HCT) on disease activity in a patient with multiple sclerosis (MS).Case report, prospective study, and autopsy.Departments of Clinical Neurosciences, Internal Medicine, and Pathology at the University of Calgary, Alberta, Canada.A 39-year-old woman with chronic myelogenous leukemia and concurrent mild MS.Hematopoietic cell transplantation from a healthy unrelated donor.After HCT the patient developed graft-vs-host disease and experienced worsening, but not new, neurological symptoms. Her circulating leukocytes were 100% of donor origin. Magnetic resonance imaging showed increased lesion burden. She died of adenovirus hepatitis 20 weeks after HCT. An autopsy revealed demyelinating-inflammatory activity in active lesions and chronic active lesions.Despite high-dose, cytotoxic, immunosuppressive therapy and exchange of a presumed autoreactive immune system with a healthy immune system, MS in this patient continued to be active.