Clear cell ependymoma is a rare and diagnostically challenging subtype of ependymoma, whose genetic features are essentially unknown. We studied 13 clear cell ependymomas (five cases WHO grade II, eight cases WHO grade III) by comparative genomic hybridization (CGH). Chromosomal imbalances were found in 12/13 cases. The most common aberrations overall were þ 1q (38%), À9 (77%), À3 (31%), and À22q (23%). Clear cell ependymomas of WHO grade II were characterized by À9 (40%), whereas WHO grade III cases mainly showed þ 1q (63%), and þ 13q (25%), as well as À9 (100%), À3 (38%), and À22q (25%). In contrast to other ependymal tumors, clear cell ependymomas of WHO grade II showed fewer imbalances than WHO grade III samples (1.4 vs 3.5 per case). Although some of the implicated chromosomes have previously been shown to be involved in other ependymoma variants, the striking frequency of þ 1q, À9, and À3 suggests that aberrations differ between clear cell and other types of ependymomas, in particular, for loss of chromosome 9 which can be regarded as the molecular hallmark of clear cell ependymomas. Modern Pathology (2006) 19, 958-962.