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Although domestic dogs were the first domesticated species, the nature of dog domestication remains a topic of ongoing debate. In particular, brain and behavior changes associated with different stages of the domestication process have been difficult to disambiguate. Most modern Western breed dogs possess highly derived physical and behavioral traits because of intense artificial selection for appearance and function within the past 200 years. In contrast, premodern dogs, including primitive/ancient breeds, village dogs, and New Guinea Singing Dogs, have undergone less intensive artificial selection and retain more ancestral characteristics. Consequently, comparisons between modern and premodern dogs can shed light on brain and behavior changes that have occurred recently in the domestication process. Here, we addressed this question using a voxel-based morphometry analysis of structural MRI images from 72 modern breed dogs and 13 premodern dogs (32 females). Modern breed dogs show widespread expansions of neocortex and reductions in the amygdala and other subcortical regions. Furthermore, cortical measurements significantly predicted individual variation in trainability, while amygdala measurements significantly predicted fear scores. These results contrast with the long-standing view that domestication consistently involves reduction in brain size and cognitive capacity. Rather, our results suggest that recent artificial selection has targeted higher-order brain regions in modern breed dogs, perhaps to facilitate behavioral flexibility and close interaction and cooperation with humans.