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In this brief, a methodology for detection and accommodation of actuator faults for a class of multi-input-multi-output (MIMO) stochastic systems is presented. First, a new real-time fault estimation module that estimates the actuator effectiveness is developed. The actuator fault diagnosis is based on the estimation of the state vector. Under some conditions, the stochastic system is transformed into two separate subsystems. One of them is not affected by actuator faults, so a reduced order Kalman filter can be used to estimate its states. The other, whose states are measurable, is affected by the faults. Then, the output of the nominal controller is reconfigured to compensate for the loss of actuator effectiveness in the system. Simulation results of a helicopter in vertical plane is presented to demonstrate the performance of the proposed fault-tolerant control scheme.