The paper addresses the fault detection problem for discrete event systems in a Petri Net (PN) framework. Assuming that the structure of the PN model and the initial marking are known, faults are modelled by unobservable transitions. Moreover, we assume that there may be additional unobservable transitions associated with the system legal behaviour and that the marking reached after the firing of any transition is unknown. The proposed diagnoser works on-line: it waits for the firing of an observable transition and employs an algorithm based on the definition and solution of some integer linear programming problems to decide whether the system behaviour is normal or exhibits some possible faults. The results characterize the properties that the PN modelling the system fault behaviour has to fulfill in order to reduce the on-line computational effort. (C) 2009 Elsevier Ltd. All rights reserved.