A flexible manufacturing system (FMS) is an application of modern manufacturing techniques. Like for other manufacturing equipment, the success of an FMS is very much dependent upon its trouble-free operation. It is crucial to monitor all the possible faults or abnormalities in real time and, when a fault is detected, react quickly in order to maintain the productivity of the FMS. Because of the complexity of FMSs, the functionally complete diagnosis of an FMS should be based on all the available information and various advanced diagnostic techniques so as to get a satisfactory result. This paper proposes a systematic approach to fault diagnosis of FMSs that integrates condition monitoring, fault diagnosis and maintenance planning. An intelligent integrated fault-diagnosis system is designed with a modular and reconfigurable structure. The implementation of the integrated diagnosis system is presented in detail. The system can monitor the major conditions and diagnose the major faults of an FMS, and give corresponding maintenance planning as well. The developed system has been applied to an existing FFS-1500-2 FMS in Zhengzhou Textile Machinery Plant and has achieved good results.