PROBLEM TO BE SOLVED: To provide a method for accurately and stably determining whether a subject is affected with chronic fatigue syndrome or not.SOLUTION: There is provided a method for determining whether a subject is affected with chronic fatigue syndrome or not, which comprises: a step of measuring the expression amount of gene transcript of at least one gene each belonging to at least two gene groups selected from an energy production-related gene group, a virus infection-related gene group, a cell death-related gene group, an antioxidation-related gene group, an immune function-related gene group and an iron regulation-related gene group, in a biological sample; a step of obtaining as an average a value representing a deviation of the one gene from the expression amount of the measured gene transcript, based on the expression amount of the corresponding gene transcript in a population of healthy subjects, or obtaining the average of the values representing the deviation of two or more genes when obtaining values representing deviations of two or more genes belonging to selected gene groups; and a step of determining whether the subject is affected with the chronic fatigue syndrome or not by using the average.