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This paper presents a methodology for integrated reliability evaluation of distribution and sub-transmission systems with the presence of distributed generation (DG) based on different energy sources. The methodology considers the possibility of DG connection at the High Voltage (HV) and Medium Voltage (MV) buses of the distribution substation, as well as along the MV distribution network. The uncertainty of energy availability of time varying energy sources, such as the wind generation, and the chronological variation of the loads are included in the methodology. The network representation includes the main protection and reconfiguration devices, such as breakers, manual switches, automatic sectionalizers, reclosers and fuses. Some operative polices in relation to DG, such as islanded operation, protection schemes for network failures, etc. are analyzed, as well as load shedding prioritization and load transfer between feeders. The system reliability evaluation is based on Sequential Monte Carlo Simulation. The reliability indexes calculated are the load point average failure rate (lambdaL) and the annual outage time (UL) and the system indices SAIFI, SAIDI, EENS and ECOST. Results for the RBTS system and for an actual Brazilian distribution network are presented.