Eukaryotic Topoisomerase II (Topo II) is present in two isoforms alpha and beta. The alpha isoform is predominantly localized in proliferative tissue, while beta isoform is present in all tissues. In the present study we report the activity and protein levels of Topoisomerase II alpha and beta in rat brains of different age groups viz.: E11 (Embryo day 11), E18 (Embryo day 18), post-natal day 1, young (<10 days), adult (<6 months) and old (>2 years). Topoisomerase II beta isoform is found to be the predominant form in brain tissue but Topoisomerase II alpha is found in embryos up to post-natal day 1. The studies to examine the regional distribution of Topoisomerase II beta in brain showed highest activity in cerebellar region and that too only neuronal cell fraction. There was a significant age-dependent decline in this activity. Hence, Topoisomerase II beta may have some unknown function in cerebellum and the low levels of Topoisomerase II beta activity in ageing cerebellum may contribute to the genomic instability in cerebellar region of ageing brain.