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A fault detection and diagnosis (FDD) and a fault-tolerant control (FTC) system for an unmanned aerial vehicle (UAV) subject to control surface failures are presented. This FDD/FTC technique is designed considering the following constraints: the control surface positions are not measured and some actuator faults are not isolable. Moreover, the aircraft has an unstable spiral mode and offers few actuator redundancies. Thus, to compensate for actuator faults, the healthy controls may move close to their saturation values and the aircraft may become uncontrollable; this is critical due to its open-loop unstability. A nonlinear aircraft model designed for FTC researches has been proposed. It describes the aerodynamic effects produced by each control surface. The diagnosis system is designed with a bank of unknown input decoupled functional observers (UIDFO) which is able to estimate unknown inputs. It is coupled with an active diagnosis method in order to isolate the faulty control. Once the fault is diagnosed, an FTC based on state feedback controllers aims at sizing the stability domain with respect to the flight envelope and actuator saturations while setting the dynamics of the closed-loop system. The complete system was demonstrated in simulation with a nonlinear model of the aircraft.