Abstract: Methods for the diagnosis and treatment of chronic fatigue syndrome (CFS) are disclosed based upon the finding that particular individual acylcarnitines are present in modified concentrations (ie decreased or increased concentrations) in CFS patients compared to healthy control subjects. In one form of the invention, a diagnostic method comprises determining a concentration of at least one individual acylcarnitine compound (eg oleyl-L-carnitine and linoleyl-L-carnitine) in a body sample from a test subject and comparing the concentration to a reference concentration, wherein a difference in the concentration of the at least one individual acylcarnitine from the test subject compared to the reference concentration is indicative of CFS.