Brain structures with bioelectric activity (BA) different from BA of the same structures in healthy peers were revealed using an original 3DLocEEG analysis of EEGs that solves so-called “reverse EEG task”. These were the following structures: thalamus, pineal gland, hypothalamic area, including suprahiasmatic nuclei, and infratemporal cortex. The shift of BA focus to structures of the left hemisphere including left thalamus was recorded in patients with AIS; the shift increased both with worsening of deformation and increasing progression activity. This was not observed in healthy children (aged 7–14 years), although it is natural for older adolescents (15–17 years) and healthy adults. In other words, the interhemispheric asymmetry of brain BA in children with AIS becomes typical for the definitive brain much earlier. This phenomenon may be used for future development of a method for prediction of deformation progression patterns. A number of differences obtained in comparative analysis of EEGs, processed by 3DLocEEG method, between right-side and left-side AIS allow us to hypothesize about aetiology and pathogenesis differences of these two AIS clinical forms. Data obtained suggest that brain structures play a much more important role in aetiology and pathogenesis of AIS right-side forms compared with left-side ones. Primary subclinical dysfunctions of brain regulatory systems leading to disturbances of spinal cord and brain associated growth and subsequently to scoliosis development are supposed to play the main role in pathogenesis of right-side AIS forms (or their substantial part). Evidently, the major reason for manifesting these latent dysfunctions is an overstrain of central nervous system (CNS) adaptation-compensation mechanisms during the pubertal period.