Purpose: Prelingual deafness has been shown to lead to brain reorganization as demonstrated by functional parameters, but anatomical evidences still remain controversial. The present study investigated hemispheric asymmetry changes in deaf subjects using MRI, hypothesizing auditory-, language- or visual-related regions after early deafness. Methods: Prelingually deaf adolescents (n = 16) and age- and gender-matched normal controls (n = 16) were recruited and hemispheric asymmetry was evaluated with voxel-based morphometry (VBM) from MRI combined with analysis of cortical thickness (CTh). Results: Deaf adolescents showed more rightward asymmetries (L < R) of grey matter volume (GMV) in the cerebellum and more leftward CTh asymmetries (L > R) in the posterior cingulate gyrus and gyrus rectus. More rightward CTh asymmetries were observed in the precuneus, middle and superior frontal gyri, and middle occipital gyrus. The duration of hearing aid use was correlated with asymmetry of GMV in the cerebellum and CTh in the gyrus rectus. Interestingly, the asymmetry of the auditory cortex was preserved in deaf subjects. Conclusions: When the brain is deprived of auditory input early in life there are signs of both irreversible morphological asymmetry changes in different brain regions but also signs of reorganization and plasticity which are dependent on hearing aid use, i.e. use-dependent.