A 13-year-old girl with a ten-year history of lymphoblastic leukemia and several central nervous system (CNS) relapses developed a bone marrow relapse and accelerated CNS leukemia. Following treatment with CNS radiation and intravenous chemotherapy, she developed fever, pancytopenia, headache, and vomiting. Her neurological function deteriorated and she died on the 20th hospital day. Multiple CSF examinations failed to disclose either leukemic cells or organisms. Blood cultures obtained from a Broviac catheter yielded Micrococcus species. Postmortem examination showed meningoependymitis with intracellular coccal organisms. The pathology of this infection resembles intracranial Whipple's disease. Intracranial intracellular bacterial infection should be excluded in the infectious complications in the immunocompromised host.