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This paper presents a stochastic framework for the optimization of microgrids that has the functionality of providing flexibility services to System Operators (SOs) considering uncertainties in the energy forecast. The methodology is developed with the aim of being applied to complex microgrids composed of different distributed energy resources and hybrid energy storage systems (ESS). The associated optimization problem is operated in two stages: the first one performs a stochastic optimization of the microgrid in order to reserve an up/down regulation capacity with which to deal with the energy forecast uncertainties of the microgrid. The different microgrid devices are optimized by considering their operational costs in order to achieve their optimal operation in the Day-Ahead Market (DM). The second stage is used to re-schedule the initial planning according to the signal request and an economic offer from the SO. The control problem is developed using Stochastic Model Predictive Control (SMPC) techniques and Mixed-Integer Quadratic Programming (MIQP), owing to the presence of logic, integer, mixed and probabilistic variables. The simulation results show that the proposed methodology reduces the risk of undergoing up/down-penalty deviations in the Regulation Service Market (RM), also being able to provide flexibility services to the SOs, despite being subject to uncertainties in the energy forecast carried out for the microgrid. [ABSTRACT FROM AUTHOR]