The definition of border cluster is clarified on the basis of relevant literature review. The author made SWOTanalysis of conditions and opportunities of the border clusters creation with involvement of the Russian and the Kazakh cross-border regions. The cluster formations are viewed as one of the interregional cooperation forms. The author identifies the particular characteristics and requirements of the border clusters aimed at intensification of the Russian-Kazakh economic partnership. The paper defines the prospects of participation of border regions of the Siberian Federal District in cluster initiatives under the Customs Union of Russia, Kazakhstan and Belarus. The author offers the business lines of potential border clusters: industrial (energetic, agro industrial), innovative and technological (biopharmaceutical), tourist, transport and logistics considering M. Porter»s methodology of the analyses of the potential and developing clusters, key elements of cluster policy in cross-border regions in Russia and Kazakhstan, economic and social relations in external environment of the common states.