Observation of sub-clinical neurological abnormalities has led to the proposal of a neuro-developmental etiologic model for AIS. Our research group have demonstrated longer latency in somatosensory–evoked potential (SSEP) and impaired balance control in AIS subjects. A previous pilot study compared the regional brain volume between right thoracic AIS subjects and normal controls. Significant regional brain differences were found relating to corpus callosum, premotor cortex, proprioceptive and visual centers. Most of these regions involved the brain unilaterally, indicating there might be abnormal asymmetrical development in the brain in right thoracic AIS. In this pilot study, we investigated whether similar changes are present in left thoracic AIS patients who differ from matched control subjects. Nine AIS female patients with atypical left thoracic AIS (mean age 14.8, mean Cobb angle 19°) and 11 matched controls as well as 20 right thoracic AIS (mean Cobb angle 33.8°) and 17 matched controls, underwent three-dimensional isotropic magnetization prepared rapid acquisition gradient echo (3D_MPRAGE) magnetic resonance (MR) imaging of the brain. Fully automatic morphometric analysis was used to analyse the MR images; it included brain-tissue classification into grey matter (GM), white matter (WM) and cerebrospinal fluid (CSF). and non-linear registration to a template brain. Tissue densities were compared between AIS subjects and controls. There was no significant difference between AIS subjects and normal controls when comparing absolute and relative (i.e. brain-size adjusted) volumes of grey and white matter. Using voxel-based morphometry, significant group differences (controls > left AIS) were found in the density of WM in the genu of the corpus callosum, the left internal capsule (anterior arm) and WM underlying the orbitofrontal cortex of the left hemisphere. The above differences were not observed in the right AIS group. This first controlled study of regional tissue density showed that corpus callosum, which is the major commissural fiber tract, was different in the atypical left thoracic scoliosis while significant regional brain changes have not yet been found in those with typical right thoracic scoliosis. Further investigation is warranted to see whether the above discrepancy is related to laterality of the scoliotic curves and infratentorial neuroanatomical abnormalities. A larger sample and a longitudinal study is required to establish whether the brain abnormalities are predictive of curve progression.