Facioscapulohumeral muscular dystrophy (FSHD), a pathology primarily characterized by involvement of the muscles in the face, shoulder and upper arm, can be associated to several CNS disorders, including sensorineural hearing deficits, schizophrenia, epilepsy and mental retardation. Aim of our study was to verify if brain tissue volumes, as measured by segmentation of MRI studies, are altered in FSHD. Volumes of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF) were compared, taking into account head size age and sex, both globally (by multiple regression analysis) and regionally (by optimized voxel-based morphometry-VBM) in thirty patients with FSHD and 39 normal subjects (NS). FSHD patients had significantly lower GM volumes and higher CSF volumes (P < 10(-4)). GM loss showed a borderline correlation with clinical severity (P < 0.05). Brain tissue volumes did not correlate with disease duration, size of the genetic deletion, age at onset and the presence at MRI of WM hyperintensities (detected in 4/22 patients). At VBM three clusters of GM loss were detected, in the left precentral cortex (Brodmann areas 6, 2 and 44, P < 10(-14) corrected for multiple comparisons at cluster level), in the anterior cingulate (Brodmann areas 33, 24 and 11, P < 10(-4)) and in the right fronto-polar region (Brodmann area 10, P < 5.10(-3)). To the best of our knowledge, this is the first study to demonstrate a reduction in GM volume in FSHD. We hypothesize that localized GM loss in FSHD is the consequence of a selective involvement of specific CNS structures.