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In recent years we have witnessed an increased interest for installations of hybrid energy supply systems in buildings, designed specifically to meet their diverse energy demand (cooling, heating and electricity). This paper proposes a new algorithm that generates the optimal hybrid energy system mix and suggests the ways for the system normal operation. The integrated approach analyzes simultaneously the end-use energy demand, primary energy sources and available storage technologies. This integration has been only made possible by the recent advances in SmartGrids technology offering more flexibility in selection and management methods of installed energy sources and loads. A case study is used to present the capability of the algorithm to find an optimal system structure from a large mix of alternative solutions. Such thorough and holistic approach, as proposed in this paper, has not been yet reported in the literature or implemented in any existing modeling and design tools.