To explore the possible molecular interaction between CK2 and PrP, the full length sequences of human CK2alpha and CK2beta genes were amplified with RT-PCR using the mRNA from cell line SH-SY5Y as the template, and then the fusion proteins HIS-CK2alpha and GST-HIS-CK2beta were expressed in E. coli. The interaction between CK2 and PrP was evaluated with immunoprecipitation and pull-down assays. The results demonstrated that recombinant PrP bound specifically with CK2alpha, but not with CK2beta. The native CK2 and PrP in the hamster brains interacted each other, forming protein complexes. The domain responsible for interacting with CK2alpha was located at the C-terminal segment of PrP (residues 90-231). This study proposed reliable experimental data for the molecular interaction between PrP and CK2alpha, both in recombinant and native categories. These results supply scientific clues for further assessing the potential biological significance of the interaction of PrP with CK2 and possible role of CK2 in the pathogenesis of prion diseases.