Correction of psychoemotional and autonomic disturbances in children 7-17 years old with diabetes mellitus type 1 was conducted using transcranial magnetic electro-stimulation with alternate action on brain hemispheres (main group, 42 patients). The method includes the combined action of magnetic field pulses and series of electric impulses; magnetic and electric stimulation were performed synchronously - at first, on one brain hemisphere, then on another hemisphere with alternation frequency 9.5-10.5 Hz. A comparison group consisted of 44 patients with diabetes mellitus type 1 who received physiotherapeutic treatment as a combination of transcranial magnetic therapy and electro-stimulation with simultaneous action on both brain hemispheres. Treatment duration was 10 sessions. Treatment efficacy was assessed by the decrease in frequency and intensity of complaints, improvement of patient's health status measured (a scale for assessment of activity, health perception and mood) and improvement of the status of the autonomic nervous system (Vein's questionnaire), mental sphere (the Luscher color test) and cognitive traits (The Concentrated Attention Test of the Toulouse-Pierron Factorial Battery). The status of the autonomic nervous system was evaluated before and after the treatment using cardiointervalography. Brain bioelectrical activity was assessed using encephalography. Significant reduction of autonomic, psychoemotional and cognitive disturbances, normalization of brain bioelectrical activity due to the -rhythm organization and arrhythmia removal were identified in the main group after the treatment. No adverse effects of this physiotherapeutic treatment was found.