Abstract: Methods for diagnosing and treating chronic fatigue syndrome in a patient comprise, for example, testing tissue of the patient for the presence of nucleic acid molecules of one or more CFS-causing herpesviruses and one or more non-herpesvirus infectious agents, and diagnosing the patient's CFS as (a) caused by one or more herpesvirus and no non-herpesvirus infectious agent; (b) caused by one or more herpesviruses and at least one non-herpesvirus infectious agent; (c) not caused by a herpesvirus and caused by at least one non-herpesvirus infectious agent; and (d) not caused by a herpesvirus and not caused by at least one non-herpesvirus infectious agent. In some embodiments, the methods of treating comprise administering a therapeutically effective amount of at least one pharmaceutical composition for each herpesvirus and/or non-herpesvirus infectious agent present found in the patient.