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Much of cognitive research on deductive reasoning has been preoccupied with advocating for or against visuospatial (mental model theory) or linguistic/syntactic (mental logic theory) models of logical reasoning. Neuroimaging studies bear on this issue by pointing to both language-based and visuospatial systems being engaged during logical reasoning, and by raising additional issues not anticipated by these cognitive theories. Here, the literature on the neural basis of deductive reasoning from the past decade is reviewed. Although these results might seem chaotic and inconsistent, we identify several interesting patterns and articulate their implications for cognitive theories of reasoning. Cognitive neuroscience data point away from a unitary system for logical reasoning and towards a fractionated system dynamically reconfigured in response to specific task and environmental cues.