This cutting-edge review of the orexin/hypocretin system sets the stage for advanced research on the pathological mechanisms underlying the loss of orexin/hypocretin neurons in humans, regulation of sleep and wakefulness by the orexin/hypocretin system, and the role of the orexin/hypocretin system in many other physiological processes, including feeding, autonomic regulation, and neuroendocrine regulation. The authors also introduce several experimental methods for orexin/hypocretin research, and, using multidisciplinary approaches, explain their uses and limitations. Contents: Part I. History. History and Overview of Orexin/Hypocretin Research: From Orphan GPCR to Integrative Physiology. Part II. Overview of the Orexin/Hypocretin Neuronal System. Orexin and Orexin Receptors. Orexin Projections and Localization of Orexin Receptors. Neural Responses to Hypocretin/Orexin. Afferent Systems of Orexin Neurons. Part III. Assessment of Orexins/Hypocretin Functions in Tissue and Biological Fluids. Hypocretin Measurements in the CSF, Blood, and Brain Tissues: Basic and Clinical Applications. Hypocretin Receptor-Activated G Proteins Revealed by [35S]GTPgS Autoradiography. Part IV. Physiology. A. Orexin/Hypocretin System and Hypothalamic Function. Orexin System and Feeding Behavior. Orexins and the Autonomic Nervous System. Neuroendocrine Role of the Orexins (Hypocretins). Orexin/Hypocretin System and Stress and Emotion. B. Orexins/Hypocretins and Sleep Regulation. Hypocretin as a Wakefulness Regulatory Peptide. Hypocretin/Orexin Tonus and Vigilance Control. Hypocretin System and Aminergic and Cholinergic Systems in the Control of Vigilance. Orexin and Hypothalamic Control of Sleep and Waking. Hypocretin/Orexin and Motor Function. Part V. Pathophysiology: Narcolepsy and Orexin/Hypocretin Deficiency. A Orexin/Hypocretin Deficiency and Narcolpesy. Overview of Human Narcolepsy. Canine Models of Narcolepsy. Rodent Models of Human Narcolepsy-Cataplexy. B. Orexin/Hypocretin Deficiency in Human Narcolepsy and Other Conditions. Hypocretin Deficiency in Human Narcolepsy: Mutation Screening, Neuropathology, and CSF Hypocretin-1 Level. Hypocretin Status in Neurological Disorders in Relation to Excessive Sleepiness and Cataplexy. Hypocretin Measures in Psychiatric Disorders. Neuroendocrinology of Human Narcolepsy. Narcolepsy and Autoimmunity. C. Treatment/Pharmacology. Pharmacology of Orexin/Hypocretin Peptides and Small Molecules. Ectopic Overexpression of Orexin Peptides in Mouse Brains: Implications for Future Treatment of Narcolepsy-Cataplexy. Hypocretin/Orexin Replacement Therapy in Hypocretin/Orexin-Deficient Narcolepsy: An Overview.