The histaminergic neuron system in the brain has been well-characterized in the last twenty years. This article describes the studies performed by our research groups and discusses the physiological functions of the histaminergic neurons. To demonstrate the distribution of neuronal antibodies against histidine decarboxylase (HDC), the sole enzyme responsible for histamine formation, was used, although the purification of the HDC from fetal rat liver was a difficult task. It took five years to purify the enzyme and another five years to obtain specific antibody suitable for immunohistochemistry. The cell bodies were located in the tuberomammillary nucleus of the posterior hypothalamus. The clusters of cell bodies were designated as E1-5 groups. The fibers that projected from the neurons were distributed in almost all parts of the brain, especially densely in the anterior hypothalamus. α-Fluoromethylhistidine, a specific inhibitor of HDC, is a powerful tool for reducing the neuronal histamine in the brain. Administration of α-fluoromethylhistidine led to changes in various activities of the brain such as arousal state, circadian rhythm, neuroendocrine functions, feeding behavior, body temperature, and vestibular function. These results indicate that the histaminergic neuron system regulates a wide range of physiological functions in the brain by targetting both neurons and glial cells, on which we found histamine H1 and H2 receptors. The molecular structure of the H1-receptor was also discussed.