Ependymoblastomas are very rare and highly malignant embryonal tumours of the central nervous system with distinctive multilayered rosettes being the main histopathological feature. They are a diagnostically challenging subtype of embryonal tumours, whose genetic features are unknown. Primary ependymoblastomas from four children (one boy, three girls; mean age 24.8 months, range 4-41 months) were investigated by comparative genomic hybridisation (CGH), to our knowledge constituting the only cohort of this entity studied by cytogenetic means. DNA copy number changes were found in each case, consisting mainly of gains of chromosome 2 as well as losses of chromosomes 6q and 13q (75% each). The tumours showed between one and five aberrations with a mean of 3.25 DNA copy number changes per case, with gains being less frequent than losses (1.25 gains vs 2 losses per case). The youngest patient showed the least imbalances (one), whereas the oldest child presented with the most aberrations (five). Clinical follow-up data were available for three of the four patients. All three had died of their disease after a post-operative survival of 9 months (range 6-14 months). Our CGH data suggest that ependymoblastomas show distinct and fairly consistent chromosomal aberrations.