Recently an unmanned aerial vehicle (UAV) has been widely used for military and civil applications. The role of a navigation system in the UAV is to provide navigation data to the flight control computer (FCC) for guidance and control. Since performance of the FCC is highly reliant on the navigation data, a fault in the navigation system may lead to a disastrous failure of the whole UAV. Therefore, the navigation system should possess a fault detection and isolation (FDI) algorithm. This paper proposes an attitude determination GPS/INS integrated navigation system with an FDI algorithm for a UAV. Hardware for the proposed navigation system has been developed. The developed hardware comprises a commercial inertial measurement unit (IMU) and the integrated navigation package (INP) which includes an attitude determination GPS (ADGPS) receiver and a navigation computer unit (NCU). The navigation algorithm was implemented in a real-time operating system with a multi-tasking structure. To evaluate performance of the proposed navigation system, a flight test has been performed using a small aircraft. The test results show that the proposed navigation system can give accurate navigation results even in a high dynamic environment.