Misophonia is a newly described condition in which specific ordinary sounds provoke disproportionately strong negative affect. Since evidence for neurobiological abnormalities underlying misophonia is scarce, we tested whether misophonia patients differed from healthy controls in grey matter volumes and resting-state functional connectivity. We collected structural magnetic resonance imaging and resting-state functional magnetic resonance imaging data from 24 misophonia patients and 25 matched controls. Compared to controls, voxel-based morphometry showed larger right amygdala volume in misophonia patients. Follow-up seed-based functional connectivity analysis of the amygdala showed a different pattern of connectivity with the cerebellum, driven by greater connectivity with the left amygdala. Additional data-driven independent component analysis showed greater connectivity within lateral occipital cortices and fusiform gyri in the ventral attention network. We propose that the amygdala enlargement may be associated with heightened emotional reactivity in misophonia. The higher connectivity between left amygdala and cerebellum might be linked to a tendency to exhibit reflex-like physical reactions to triggers. Higher attention network connectivity may reflect sensory enhancement of visual triggers or visual imagery related to trigger sounds. In sum, we found structural and functional abnormalities which implicate dysfunction of emotional and attentional systems in misophonia.