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Recent research activities on cognitive radio (CR) have mainly focussed on opportunistic spectrum access and spectrum utilization. However, CR technology will have a significant impact on upper layer performance in wireless networks, particularly in mobile ad hoc networks (MANETs). In this paper, we study topology control and routing issues in CR-MANETs and propose a distributed prediction-based cognitive topology control (PCTC) scheme to provision cognition capability to routing in CR-MANETs. PCTC is a middleware-like cross-layer module residing between CR module and routing. It uses cognitive link availability prediction, which is aware of the interference to primary users and user mobility, to predict the available duration of links. Based on the link prediction, PCTC captures the dynamic changes of the topology and constructs an efficient and reliable topology, which is aimed at mitigating rerouting frequency and improving end-to-end network performance such as throughput and delay. Simulation results are presented to show the effectiveness of the proposed scheme.