Abstract We used ultra-high field (7 Tesla) magnetic resonance imaging (MRI) at submillimeter resolution to assess structural brain changes in congenitally blind (CB) compared to matched normal sighted control (SC) subject groups. Region-of-interest analysis revealed grey matter (GM) volumetric reductions in the CB group in left cuneus and occipital pole, right posterior collateral sulcus and right occipito-temporal medial lingual sulcus. Non-visual areas with GM reductions in CB included the left central, postcentral and superior frontal gyri, and the right subcallosal gyrus. In contrast, there were no significant group differences in cortical thickness when using stringent statistical criteria. Regional differences in white matter (WM) showed an overall pattern similar as that of GM changes, characterized by volume reductions in occipital, parietal and temporal areas, but with additional reductions in precuneus and medial orbitofrontal cortex. Differences in cortical curvature were mostly situated in the occipital cortex and bore a close relationship with areas showing GM alterations; they may be indicative of increased cortico-cortical connectivity of the visually-deprived occipital cortex. The CB group had GM reductions in the basal ganglia, i.e., caudate nucleus, putamen, nucleus accumbens, globus pallidus, and thalamus. Within the cerebellum, GM and WM volumes were also reduced in the CB. Segmentation of the thalamus, hippocampus and amygdala into anatomic divisions revealed GM reductions in a number of thalamic nuclei, a few hippocampal regions, but not within amygdala. There were no findings of increased volume or cortical thickness in the CB group. Together, these data reveal a multitude of GM and WM reductions in CB, comprising not only the occipital cortex, but also temporal, parietal, and prefrontal cortices, as well as the basal ganglia and cerebellum. These findings in the CB may seem at odds with the large literature showing that the visually-deprived occipital cortex becomes a multimodal cortex responding to diverse non-visual sensory and cognitive inputs. The seeming mismatch between morphological atrophy and enhanced multimodality of occipital areas combined with superior performance by the CB in various non-visual tasks poses a challenge for our understanding of brain plasticity.