Protein kinase CKII is composed of two catalytic (alpha or alpha') subunits and two regulatory (beta) subunits. The CKIIbeta subunit is thought to mediate the tetramer formation and interact with other target proteins. Previously we have shown that CKIIbeta interacts with ribosomal proteins L5 and L41, DNA topoisomerase IIbeta, and SAG/CKBBP1. In this study, the two-hybrid system was used to define the subregions of CKIIbeta that are involved in the interaction with L5, L41, topoisomerase IIbeta, SAG/CKBBP1, and unknown proteins, CKBBP2 and CKBBP3. The results indicated that the region between residues 1 and 167 of CKIIbeta is common binding site for L5, topoisomerase IIbeta, SAG/CKBBP1, and L41. The region between amino acids 19 and 167 of CKIIbeta is sufficient for the interaction with CKBBP3. The region between residues 67 and 130 of CKIIbeta is a minimal fragment that is required for interaction with CKBBP2. Overlay experiments showed that the region between residues 1 and 167 of CKIIbeta interacts with L5, L41, and SAG/CKBBP1 in vitro. These results suggest that the binding sites of CKIIbeta for these target proteins are not located within a small linear sequence stretch, but rather are created by a three-dimensional structure.