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Recently, research interest has increased in the design, development, and deployment of mobile agent systems for high-level inference and surveillance in a wireless sensor network (WSN). Mobile agent systems employ migrating codes to facilitate flexible application re-tasking, local processing, and collaborative signal and information processing. This provides extra flexibility, as well as new capabilities to WSNs in contrast to the conventional WSN operations based on the client-server computing model. In this article we survey the potential applications of mobile agents in WSNs and discuss the key design issues for such applications. We decompose the agent design functionality into four components, that is, architecture, itinerary planning, middleware system design, and agent cooperation. This taxonomy covers low-level to high-level design issues and facilitates the creation of a component-based and efficient mobile agent system for a wide range of applications. With a different realization for each design component, it is expected that flexible trade-offs (e.g., between energy and delay) can be achieved according to specific application requirements.