We report a patient who achieved hematologic response with Imatinib mesylate and is in chronic phase, but after several years developed neurologic symptoms and was eventually documented to have an isolated CNS relapse. The patient was treated with intrathecal chemotherapy to clear the spinal fluid of the leukemia cells. Imatinib mesylate (STI-571) is a potent and selective inhibitor of BCR-ABL tyrosine kinase and has emerged as a treatment of choice in chronic myeloid leukaemia. However because of poor penetration of the drug to the blood-brain barrier of the central nervous system (CNS), then the CNS acts as a sanctuary site for malignant cells.