Research on political judgment and decision-making has converged with decades of research in clinical and social psychology suggesting the ubiquity of emotion-biased motivated reasoning. Motivated reasoning is a form of implicit emotion regulation in which the brain converges on judgments that minimize negative and maximize positive affect states associated with threat to or attainment of motives. To what extent motivated reasoning engages neural circuits involved in “cold” reasoning and conscious emotion regulation (e.g., suppression) is, however, unknown. We used functional neuroimaging to study the neural responses of 30 committed partisans during the U.S. Presidential election of 2004. We presented subjects with reasoning tasks involving judgments about information threatening to their own candidate, the opposing candidate, or neutral control targets. Motivated reasoning was associated with activations of the ventromedial prefrontal cortex, anterior cingulate cortex, posterior cingulate cortex, insular cortex, and lateral orbital cortex. As predicted, motivated reasoning was not associated with neural activity in regions previously linked to cold reasoning tasks and conscious (explicit) emotion regulation. The findings provide the first neuroimaging evidence for phenomena variously described as motivated reasoning, implicit emotion regulation, and psychological defense. They suggest that motivated reasoning is qualitatively distinct from reasoning when people do not have a strong emotional stake in the conclusions reached.