Abstract: In this paper, fault detection and isolation in the integarted navigation system are discussed. And the 5 stage fault detection algorithm, in cluding built in test (BIT), rationality test for outputs of sub systems, correlation test among outputs of sub systems, test for residuals in Kalman filter and rationality test for estimation of error obtained by Kalman filter, is proposed. This algorithm is effective and can be easily implemented with low computation cost. It has been applied to integrated navigation system and increases its reliability remarkably.