This paper presents a novel health monitoring and fault adaptive control architecture for an unmanned hexrotor helicopter. The technologies developed to achieve the described level of robust fault contingency management include; 1.) A Particle Swarm Optimization (PSO) routine for maximizing the “built-in” fault tolerance that the closed loop flight control system affords, 2.) A two-stage Kalman filter scheme for real-time identification of faults that are masked by control system compensation, and 3.) A reconfigurable control allocation method which compensates for large degradations of the six main motor/rotor assemblies. The fault adaptive control system presented herein has strong robustness against small faults without the need for controller reconfiguration, and strong tolerance of large faults through adaptive accommodation of the fault source and severity. By taking advantage of the inherent fault-tolerant nature of typical closed loop control systems, the technology described in this paper avoids the difficulties associated with typical fault detection and isolation (FDI) techniques that have poor performance when targeting incipient faults. Simulation results show the effectiveness of the proposed approach when various levels of fault severity are seeded in one of the six main motors.