This thesis focuses on estimating faults in complex large-scale integrated aircraft systems, especially where they interact with, and control, the aircraft dynamics. A general assumption considered in the reliability of such systems is that any component level fault will be monitored, detected and corrected by some fault management capability. However, a reliance on fault management assumes not only that it can detect and manage all faults, but also that it can do so in sufficient time to recover from any deviation in the aircraft dynamics and flight path. Testing for system-level effects is important to ensure better reliability of aircraft systems. However, with existing methods for validation of complex aircraft systems, it is difficult and impractical to set up a finite test suite to enable testing and integration of all the components of a complex system. The difficulty lies in the cost of modelling every aspect of every component given the large number of test cases required for sufficient coverage. Just having a good simulator, or increasing the number of test cases is not sufficient; it is also important to know which simulation runs to conduct. For this purpose, the thesis proposes simulating faults in the system through the violation of “axiomatic conditions” of the system components, which are conditions on the functioning of these components introduced during their development. The thesis studies the effect, on the aircraft dynamics, of simulating such faults when reference models of the components representing their key functions are integrated.