Many important activities of modern society rely on the proper functioning of complex systems such as electricity networks, telecommunication networks, manufacturing plants and aircrafts. The supervision of such systems must include strong diagnosis capability to be able to effectively detect the occurrence of faults and ensure appropriate corrective measures can be taken in order to recover from the faults or prevent total failure. This thesis addresses issues in the diagnosis of large complex systems. Such systems are usually distributed in nature, i.e. they consist of many interconnected components each having their own local behaviour. These components interact together to produce an emergent global behaviour that is complex. As those systems increase in complexity and size, their diagnosis becomes increasingly challenging. In the first part of this thesis, a method is proposed for diagnosis on distributed systems that avoids a monolithic global computation. The method, based on converting the graph of the system into a junction tree, takes into account the topology of the system in choosing how to merge local diagnoses on the components while still obtaining a globally consistent result. The method is shown to work well for systems with tree or near-tree structures. This method is further extended to handle systems with high clustering by selectively ignoring some connections that would still allow an accurate diagnosis to be obtained. A hybrid system approach is explored in the second part of the thesis, where continuous dynamics information on the system is also retained to help better isolate or identify faults. A hybrid system framework is presented that models both continuous dynamics and discrete evolution in dynamical systems, based on detecting changes in the fundamental governing dynamics of the system rather than on residual estimation. This makes it possible to handle systems that might not be well characterised and where parameter drift is present. The discrete aspect of the hybrid system model is used to derive diagnosability conditions using indicator functions for the detection and isolation of multiple, arbitrary sequential or simultaneous events in hybrid dynamical networks. Issues with diagnosis in the presence of uncertainty in measurements due sensor or actuator noise are addressed. Faults may generate symptoms that are in the same order of magnitude as the latter. The use of statistical techniques,within a hybrid system framework, is proposed to detect these elusive fault symptoms and translate this information into probabilities for the actual operational mode and possibility of transition between modes which makes it possible to apply probabilistic analysis on the system to handle the underlying uncertainty present
