Malignant rhabdoid tumor (MRT) is a recently described variety of childhood renal neoplasm. MRT arising primarily in the central nervous system (CNS) is still a rather unfamiliar pathological entity and is frequently misdiagnosed as medulloblastoma or primitive neuroectodermal tumor (PNET). We describe a 7-month-old boy who harbored a CNS-MRT that originated within the IV ventricle and invaded the brain stem and the cerebellar hemispheres. After an initial documented good response to chemotherapy the tumor recurred locally 9 months after operation. We discuss clinical and histopathological features distinguishing between PNET/medulloblastoma and MRTs. Current literature on MRT of the CNS is briefly reviewed.