Hypocretins/orexins are neuropeptides involved in the regulation of sleep and energy balance in mammals. Conservation of gene sequence, hypothalamic localization of cell bodies, and projection patterns in adult zebrafish suggest that the architecture and function of the hypocretin system are conserved in fish. We report on the complete genomic structure of the zebrafish and Tetraodon hypocretin genes and the complete predicted hypocretin protein sequences from five teleosts. Using whole mount in situ hybridization, we have traced the development of hypocretin cells in zebrafish from onset of expression at 22 h post-fertilization through the first week of development. Promoter elements of similar size from zebrafish and Tetraodon were capable of driving efficient and specific expression of enhanced green fluorescent protein in developing zebrafish embryos, thus defining a minimal promoter region able to accurately mimic the native hypocretin pattern. This enhanced green fluorescent protein expression also revealed a complex pattern of projections within the hypothalamus, to the midbrain, and to the spinal cord. To further analyze the promoter, a series of deletion and substitution constructs were injected into embryos, and resulting promoter activity was monitored in the first week of development. A critical region of 250 base pairs was identified containing a core 13-base pair element essential for hypocretin expression.The hypocretin/orexin peptides (HCRT-1 and HCRT-2) 3 are neurotransmitters involved in the regulation of sleep and energy balance (1). HCRT-1 and HCRT-2 have significant homology and result from the cleavage of a common precursor encoded by the hcrt locus. In mammals, the hypocretin expressing cell clusters are located in the lateral hypothalamus and send widespread projections that innervate multiple brain areas and the spinal cord. The population is relatively small and involves ϳ70,000 neurons in the human brain (2). Projections are especially dense on several aminergic and cholinergic nuclei, most notably the adrenergic locus coeruleus and histaminergic tuberomammilary neurons (3).Loss of HCRT transmission causes the sleep disorder narcolepsy in humans, canines, and rodents (4 -6). The symptoms of narcolepsy in humans typically present in the second decade of life, usually in association with undetectable levels of HCRT-1 in the cerebrospinal fluid (7,8). Post-mortem studies indicate a 90 -95% loss of hypocretin-producing cells in human narcolepsy (2, 6, 9, 10). The process leading to cell death is unknown, but because of a strong association with human leukocyte antigen DQB1*0602 (11, 12), it is generally presumed that hypocretin cells are the target of an autoimmune process (13). This cell destruction in human narcolepsy is likely triggered by environmental factors interacting with a specific genetic background.An understanding of the processes underlying hcrt cell specification, differentiation, and maintenance as well as why they are susceptible to loss are key questions of both basic and...