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The use of autonomous systems is becoming increasingly common in many fields. A significant example of this is the ambition to deploy UAVs (unmanned aerial vehicles) for both civil and military applications. In order for autonomous systems such as these to operate effectively they must be capable of making decisions regarding the appropriate future course of their mission responding to changes in circumstance in as short a time as possible. The systems will typically perform phased missions and, due to the uncertain nature of the environments in which the systems operate, the mission objectives may be subject to change at short notice. The ability to evaluate the different possible mission configurations is crucial in making the right decision about the mission tasks that should be performed in order to give the highest possible probability of mission success.Since Binary Decision Diagrams (BDD) may be quickly and accurately quantified to give measures of the system reliability it is anticipated that they are the most appropriate analysis tools to form the basis of a reliability-based prognostics methodology. This paper presents a new Binary Decision Diagram based approach for phased mission analysis, which seeks to take advantage of the proven fast analysis characteristics of the BDD and enhance it in ways which are suited to the demands of a decision making capability for autonomous systems. The BDD approach presented allows BDDs representing the failure causes in the different phases of a mission to be constructed quickly by treating component failures in different phases of the mission as separate variables. This allows flexibility when building mission phase failure BDDs since a global variable ordering scheme is not required. An alternative representation of component states in time intervals allows the dependencies to be efficiently dealt with during the quantification process. Nodes in the BDD can represent components with any number of failure modes or factors external to the system that could affect ...