Cytogenetic and molecular studies have demonstrated that involvement of 22q is a non-random finding in malignant rhabdoid tumors (MRTs) of the brain. We present an MRT of the kidney with the karyotype 47,XY, + i(1)(q10), der(8)t(8;22)(q12;q11.2),der(22)t(8;22)(q23 or q24.1;q11.2). This unbalanced reciprocal translocation was confirmed by fluorescence in situ hybridization (FISH) with chromosome-specific paints for chromosomes 8 and 22. Molecular analysis demonstrated a partial deletion of 22q in the BCR region at q11.2, strengthening the suspicion that this is a critical region for the initiation or progression of these highly malignant neoplasms. Establishing non-random cytogenetic changes in MRTs arising from the kidney may be of value in distinguishing these rare, but often fatal tumors from other renal neoplasms that mimic them histologically. The similarity in cytogenetic and molecular abnormalities between renal and extra-renal MRTs argues against the concept that extra-renal MRTs are only representative of a rhabdoid phenotype, rather than being true rhabdoid tumors.