Background: Chronic fatigue syndrome, also known as myalgic encephalomyelitis (CFS/ME) is a particularly difficult illness to identify. To aid in classifying patients for research as well as clinical care, potential cases may be evaluated according to clinical guidelines. Purpose: The purpose of this paper is to provide an overview of three sets of guidelines currently available: the Centers for Disease Control and Prevention (CDC) Toolkit; the International Association for Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (IACFS/ME) Primer; and the International Consensus Primer. Methods: These guidelines were examined and compared with respect to required symptoms, laboratory and investigative protocols, and exclusionary and comorbid conditions. The comparisons were also intended to evaluate the guidelines in light of new research that advances the clinical understanding of CFS/ME and assists in identifying patients. Results: Guidelines vary significantly in the symptoms and comorbidities considered in light of the differing symptom requirements of three case definitions. There is also no specification on how symptoms should be measured, contributing to the significant heterogeneity found in CFS/ME. Conclusions: Further revision of clinical guidelines, preferably based on a definition that is well-informed by current empirical studies, is recommended to ensure that guidelines are applied with consistency and understanding in both research and clinical settings.