The purpose of this work is to identify a role of the pineal gland/suprachiasmatic nucleus system in adolescent idiopathic scoliosis (AIS) aetiology and pathogenesis. To analyze electroencephalograms of 292 children with AIS and in 46 healthy subjects, a processing method was used to assess three-dimensional coordinates of electric equivalent dipole sources (EEDSs) within the brain. Amounts of EEDSs in the pineal gland and suprachiasmatic nucleus (SCN) area were assessed in different age groups and during the progress of orthopaedic pathology. It was shown that children with AIS, compared with healthy children, were characterized by a higher level of electric activity (as judged by EEDS values) in the pineal gland area. It was also revealed that the number of EEDS in the pineal gland area increases significantly with increased severity of spinal deformation, while their number in the suprachiasmatic nucleus (SCN) area decreases compared with the number in healthy peers. Changes in electric activity and changes in the pineal gland and SCN area suggest that mechanisms of AIS aetiology and pathogenesis involve functional disturbances in brain areas responsible for the formation and maintenance of normal biorhythms, including osteogenesis and bone growth.