We report a malignant rhabdoid tumor (MRT) of the brain with a novel reciprocal translocation, t(12;22)(q24.3;q11.2-12). Previous reports of chromosome abnormalities in MRTs were characterized either by monosomy or partial deletions of chromosome 22. An unbalanced translocation has been identified in only a single case. To our knowledge, the present report is the first to describe a balanced reciprocal translocation in an MRT of the brain. The identification of this subtle translocation further sublocalizes the chromosomal breakpoint on chromosome 22, and could be of potential diagnostic value in cerebral MRTs.