Orexin-A and orexin-B (also known as hypocretins) are newly discovered hypothalamic peptides that stimulate food intake. Using separate radioimmunoassays for these rat orexins, we determined their distributions in microdissected nuclei of the diencephalon and brainstem which have accumulations of orexin fibers. High orexin contents (orexin-A: between 250 and 350 fmol/mg protein and orexin-B: between 650 and 900 fmol/mg protein) were present in the lateral hypothalamus; ventromedial hypothalamic, paraventricular thalamic and dorsal raphe nuclei; periaqueductal central gray and locus coeruleus. Moderate orexin contents (orexin-A: between 100 and 250 fmol/mg protein and orexin-B: between 300 and 500 fmol/mg protein) were found in the median eminence; suprachiasmatic, paraventricular hypothalamic, arcuate and supraoptic nuclei; substantia nigra and the nucleus of the solitary tract. Mature orexin-A and -B peptides were the major endogenous orexin molecules in these nuclei. The orexin-A and -B contents in the brains of obese Zucker rats that have disrupted leptin receptor were significantly higher than in their lean littermates, but in Otsuka Long-Evans Tokushima Fatty rats that have disrupted cholecystokinin type-A receptor the contents were similar to those of the controls. The widespread orexin distributions in the nuclei of diencephalon and brainstem suggest that orexins serve as neuromodulators, neurotransmitters, or both, in a wide variety of neural networks that regulate the autonomic and neuroendocrine systems.