The absence of auditory stimuli for a long period leads to modifications in brain structural and functional connectivity. However, the relationship between the brain changes and neurosensorial hearing loss is not fully clarified. In this study we considered a group of subjects with pre-lingual congenital deafness and analyzed their structural and functional connectivity. Our results suggest that auditory input deprivation not only alters the activity of sensory areas but also reshape the structural and functional organization of cognitive-related networks. These findings can be instructive to clinical practice.