It has been postulated that infants with medulloblastomas/central primitive neuroectodermal tumors (MB/PNET) may fare worse than older patients because some of them harbor unrecognized atypical teratoid/rhabdoid tumors (AT/RT), rare intracranial neoplasms that are typically unresponsive to therapy and rapidly fatal. Although small primitive cells are common to both entities, chromosome 22q11.2 deletions are common only in AT/RTs. Using fluorescence in situ hybridization (FISH) on archival, paraffin-embedded biopsy tissue with commercially available probes to 22q11.2, the region associated with RTs, we studied 8 cases of AT/RT, 12 cases of MB/PNET, and 4 cases of primitive central nervous system (CNS) neoplasms, which were difficult to classify. 22q Deletions were identified in 6 of 8 (75%) conventional AT/RTs and 0 of 12 (0%) children with classic MB/PNET. Of the 4 originally "difficult to classify" cases, 3 had deletions of 22q. In light of the FISH results, review of the morphology and immunophenotype resulted in 3 tumors being reclassified as AT/RTs and 1 as a large cell MB. These 4 cases highlight the potential diagnostic use of FISH for selected cases of primitive CNS malignancies in children and substantiate the notion that misdiagnosed AT/RTs may, in part account for the worse prognosis associated with "MB/PNET" in children younger than 2 years of age.