We report a case of primary CNS B-cell lymphoma indistinguishable from multiple sclerosis (MS). MRI of the head showed the spontaneous disappearance of the white matter lesions and the progressive cerebral atrophy. The brain biopsy failed to make a diagnosis of CNS lymphoma but rather suggested MS. Although the primary CNS lymphoma was suspected at autopsy, the immunohistochemical study showed the CNS-infiltrating lymphoid cells comprising both T-cells and B-cells. Analysis of the immunoglobulin and T-cell receptor gene rearrangements first provided evidence of primary CNS B-cell lymphoma.