In synaesthesia, stimulation of a sensory modality triggers abnormal additional perceptions. Voxel-based morphometry (VBM) was used in 18 grapheme-colour synaesthetes to investigate the neuro-anatomical basis of their abnormal perceptions. More specifically, we tested the hypothesis that in synaesthesia altered connectivity in temporo-occipital and parietal areas may be associated with grey matter (GM) changes. The data reveal increased GM volumes in fusiform and intraparietal cortices. These findings are consistent with the two-stage model of grapheme-colour synaesthesia implying cross-activation at the level of the fusiform gyrus (FG) and 'hyperbinding' at the level of the parietal cortex. The observed structural differences in grapheme-colour synaesthetes with abnormal additional perceptions may also shed some light on the neural bases of abnormal perceptions in neurological and psychiatric disorders.