Chronic fatigue syndrome (CFS) is a persistent and unexplained pathological state characterized by exertional and severely debilitating fatigue, with/without symptoms of infection or neuropsychiatric symptoms, and with a minimum duration of 6 consecutive months. The pathogenesis of CFS is not fully understood. There are no firmly established diagnostic biomarkers or treatment, due to incomplete understanding of the etiology of CFS and diagnostic uncertainty. We performed comprehensive metabolomic analyses of blood samples obtained from patients with CFS and healthy controls to establish an objective diagnosis of CFS. Here, we review previous findings concerning the immune, endocrine, and metabolic system in animal models for CFS and the patients, and present our results which may contribute to the development of a diagnostic biomarker for CFS.