The expansion of a polyQ repeat within the ataxin-2 protein causes spinocerebellar ataxia type 2 (SCA2). However, neither the precise pathological mechanism nor the physiological functions of ataxin-2 are known. Ataxin-2 contains 47 (S/T)P sequences, which are targeted by proline-directed protein kinases such as the cyclin-dependent kinase 5 (Cdk5). We hypothesized that ataxin-2 is phosphorylated by Cdk5. In fact, phosphorylation of ataxin-2 by Cdk5-p25 was shown using two methods: in vitro(32)P labeling and electrophoretic mobility shift on Phos-tag SDS-PAGE. The fractionation of ataxin-2 into three portions, the N-terminal fragment (NF, amino acids 1-507), the middle fragment (MF, amino acids 508-905), and the C-terminal fragment (CF, amino acids 906-1313) showed that NF and MF were phosphorylated slightly and highly, respectively, by Cdk5-p25 when expressed in COS-7 cells. Cdk5-mediated phosphorylation induced the degradation of NF remarkably and MF moderately. Furthermore, toxic ataxin-2-41Q underwent proteasomal degradation after phosphorylation by Cdk5. These results suggest that Cdk5 controls the abundance of both normal and polyQ-expanded ataxin-2 protein in neurons, which implies that Cdk5 activity is a therapeutic approach for SCA2.