EEG signal analysis could be very helpful in the detection of signs of adverse reaction to the brain by a systemic disease. We performed an EEG spectral analysis in 12 young patients with thalassemia before and after their regular blood transfusion, and in 10 volunteer students. Our aim was to test if the EEG analysis could detect signs of brain dysfunction due to the cerebral hypoxia as a result of the anemia. We analyzed the EEG signals on line using a dedicated computer system estimating the power of the delta, theta, alpha, sigma and beta bands of the EEG. After transfusion, the power spectral density of the alpha band showed a significant enhancement in most areas of the brain, in the group of the thalassemia patients as compared to the normals. These differences correlated with the levels of hemoglobin of the patients, and possibly reflect the degree of oxygenation of the brain. Since the visual interpretation of the EEG is not efficient for estimating the brain dysfunction in the anemic state in thalassemia, the signal analysis of the EEG may provide a more sensitive alternative to study the effects of hypoxia on brain function.