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The progressive penetration level of Distributed Generation (DG) is destined to cause deep changes in the existing distribution networks no longer considered as passive terminations of the whole electrical system. A possible solution is the realization of small networks, namely the Micro-Grids, reproducing in themselves the structure of the main production and distribution of the electrical energy system. In order to gain an adequate reliability level of the microgrids the individuation and the management of the faults with the goal of maintaining the micro-grid operation (fault tolerant operation) is quite important. In the present paper flexible power converters and a companion control algorithm for the fault tolerant operation of microgrids are presented. The effectiveness of such an algorithm and of the fault tolerant power converters are verified through computer simulations.