On the present study there are reviewed the Pineal Gland and Thymus Gland interaction and their effect on the immune system stimulation through the melatonin hormone. Starting point for the study was the response of the patients, with different brain disorders, on the application of external pico-Tesla Transcranial Magnetic Stimulation (pT-TMS). This response was potentially related with the normal function of the Pineal Gland (PG). Moreover, due to the close interaction of PG with Thymus Gland (TG) it is proposed that pT-TMS can be used so as to enhance TG effectiveness in neutralizing foreign organisms acting on human brain.