Several neuroimaging studies in developmental dyslexia (DD) have mainly focused on brain regions subserving phonological processes. However, additional deficits characterize subjects with DD, such as an impairment of visual and rapid stimuli processing and deficits in implicit learning (IL). Little is known about structural abnormalities in brain regions not directly related to phonology and reading processes. The aim of this study was to investigate, using voxel-based morphometry, whether subjects with DD exhibit any structural grey matter (GM) abnormalities in regions that have previously shown abnormal functional magnetic resonance imaging (fMRI) activation during an IL task. Significantly smaller GM volumes were found in the right posterior superior parietal lobule and precuneus and in the right supplementary motor area (SMA) of subjects with DD compared to controls. Moreover, a larger GM volume in parietal cortex was associated with an increase of IL effect in controls but not in subjects with DD. These structural abnormalities are consistent with functional changes and reinforce the hypothesis that an impairment of IL might play a relevant role in learning to read.