The article deals with the peculiarities of the cerebral organization of subcortical structures in children with autism spectrum disorders. The study involved 48 children aged from 3 to 8 years (M=5.75; SD=2.61) having ICD-10 diagnoses F84.0, F84.1, F84.5. All children underwent registration of acoustic evoked brainstem potentials and neuropsychological examination. The relationship of the indicators of acoustic evoked potentials of the brain stem with the functioning of different blocks of the brain was established: the block of cortical tone and the brain energy block (Block I), the block of reception, processing and storage of exteroceptive information (Block II), the block of programming, regulation and control of the course of mental activity (Block III). For children with difficulties in activation and energy components of activity, perception of auditory information by subcortical structures of the brain causes certain difficulties (difficulties in work of the I block of the brain). Children with difficulties in right hemispheric holistic information processing strategy and a high level of its development are characterized by a reduced level of control over the course of thought activity, with difficulties in automating thinking and speech and difficulties in coordinating movements (difficulties in the work of Block II of the brain). The identified features of the cerebral organization of the processes of perception of auditory information and processes of mental activity in children with autism spectrum disorders are manifested in disorders of the course of thought activity, the function of peripheral receptors and conduction pathways to the cortical centers of the auditory analyzer, in a lowered level of control over the auditory analyzer. In connection with these processes there are difficulties with automatization of thinking and speech, coordination of movements in children.