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The purpose of the work is to determine conflicts that may appear in clusters.

The methodology of the research is based on combination of systemic, institutional, and evolutional approaches, including private general scientific methods of subject-object, factor, comparative, functional and structural and descriptive analysis, classification, and modeling.

Comparison of programs of development of territorial innovational clusters is conducted, as well as comparative analysis of methodological approaches to analysis of the institutional basis of regional clusters; a ranking of target directions of regional programs of development of innovational territorial clusters is compiled. The authors’ classification of conflicts of regional clusters is offered.

The performed analysis helped to determine presence of various defects, dysfunctions, and negative effects with clusters that emphasize their high susceptibility to conflicts that have to be taken into account during formation of regional cluster policy, aimed at their conflict-free functioning.