We have recently discovered two novel paralogous genes from the hypothalamus of the rodents. These genes encode precursor of small neurosecretory proteins. We provisionally termed these proteins as NPGL (neurosecretory protein GL) and NPGM (neurosecretory protein GM) from C-terminal structure of each protein. In situ hybridization method shows NPGL precursor and NPGM precursor mRNAs were expressed in the lateral posterior part of the arcuate nucleus (ArcLP) and the ventral part of the tuberomammillary nucleus (TMv). In this study, we raised specific antibodies against each protein and immunohistochemical analysis was performed in the rat brain. NPGL and NPGM immunoreactive (-ir) neurons were distributed in ArcLP and TMv, and it was revealed that both peptides are produced in the same neuron. Nerve fibers of NPGL and NPGM neurons were projected to various brain regions, such as the arcuate nucleus, the ventromedial hypothalamic nucleus, the lateral hypothalamic area, the median eminence and so on. Immunoelectronmicroscopic observation revealed that NPGL or NPGM-ir vesicular structures (probably dense core vesicles) existed in the axon terminals located in the arcuate nucleus and these neurons connected with other neurons. This indicates that novel small proteins might act as neurosecretory protein. In double-fluorescence immunostaining, both novel small proteins and galanin were co-localized in more than the half of immunoreactive neurons of ArcLP. NPGL and NPGM-ir nerve fibers projected to the cell bodies of histaminergic neurons in the TMv. Furthermore, NPGL and NPGM immunoreactivities were changed by food deprivation, and c-fos protein expressions were induced in novel protein neurons. These results suggest that novel small proteins, NPGL and NPGM, may work as neurosecretory transmitter, and exert physiological function by coupling with known bioactive substances such as galanin and/or histamine.