Chronic fatigue syndrome (CFS) is a complex, multisymptom illness of unknown etiology. A variety of operational case definitions based on symptom report have been developed that share some common clinical features. Patients often come to clinical presentation after months or, more typically, years of symptomatic distress. Comorbid presentation with psychiatric illnesses has been noted. Due to these fundamental issues, the impact of patient selection and the specification of the methods of outcome assessment loom large in therapeutic studies of CFS. While a substantial body of research has focused on increasing our understanding of the basic pathobiology of CFS, there have been comparatively fewer studies that have addressed the problems of patient characterization and outcome assessment. The role of clinical methodology in the study of the therapeutics of CFS is not trivial, and may confound our understanding of pragmatic recommendations for treatment.