Chronic fatigue occurring in previously healthy children and adolescents is one of the most vexing problems encountered by pediatric practitioners. We report three cases, 11, 12 and 13-year-old children, with chronic fatigue syndrome (CFS). They initially developed a low grade fever and generalized fatigue, followed by sleep disturbance and psychosomatic symptoms, and their performance ability deteriorated. They were diagnosed as having CFS on the basis of criteria. To investigate the brain function in CFS patients, we examined the regional cerebral blood flow by single-photon emission-computed tomography (SPECT) with 111 MBq [123I]-iodoamphetamine (123I-IMP) or xenon-computed tomography (Xe-CT), and brain metabolic levels by MR spectroscopy (MRS). Blood flow, expressed as the corticocerebellar ratio (CCR), in the left temporal and occipital lobes was markedly lower in cases 2 and 3 than that in healthy subjects reported by another investigator. In case 1, however, blood flow in the left basal ganglia and thalamus was markedly higher than in healthy subjects. The MR spectroscopy (MRS) study revealed remarkable elevation of the choline/creatine ratio in the patients with CFS. None of our patients exhibited evidence of focal structural abnormalities on MRI. These findings suggest that the various clinical symptoms in CFS patients may be closely related to an abnormal brain function.