The distributions of serotoninergic neurons in the brain of the three-spined stickleback was demonstrated with the indirect peroxidase-antiperoxidase (PAP) immunohistochemical method with antibodies against serotonin. Serotoninergic perikarya were demonstrated in the brainstem reticular formation (nucleus raphe dorsalis, nucleus raphe medialis, and nucleus tegmenti dorsalis lateralis) and in the periventricular ventral thalamus and hypothalamus (nucleus ventromedialis thalami, nucleus posterioris periventricularis, nucleus recessus lateralis, and nucleus recessus posterioris). After pharmacological pretreatment of the animals with a monoamine oxidase inhibitor, serotoninergic perikarya were also visualized in area praetectalis and in the medial brainstem, caudal to nucleus raphe medialis. Whereas the cell groups of the brainstem give rise to both ascending and descending pathways, it was not possible to analyze the distribution of efferent projections from the diencephalic cell groups. Distribution of serotoninergic axons showed marked regional differences. Only scattered varicose fibers were demonstrated in the cerebellum, the facial lobes, and the lateral line lobes. In the mesencephalon, the dorsal periventricular tegmentum and the central gray receive only small numbers of serotoninergic axons, while torus semicircularis and the visual layers of tectum opticum are profusely innervated. In the diencephalon, the hypothalamus and ventral thalamus generally display the highest density of serotoninergic axons. Exceptions are found in nucleus glomerulosus and the ventromedial portion of lobus inferioris, where densities are low. In the telencephalon, the density of serotoninergic axons is very high in area dorsalis pars medialis and pars lateralis dorsalis, but low in area dorsalis pars dorsalis and pars lateralis ventralis, and intermediate in area ventralis.