The objective of this study was to clarify the 5-HT projections from the right and left sides of the dorsal (DRD), ventral (DRV) and lateral (DRL) subdivisions of the middle level of the dorsal (DR) raphe nucleus and median (MR) raphe nucleus to the lateral septum (LS), preoptic area (POA) or ventromedial hypothalamus (VMH), which are important neural substrates for neuroendocrine regulation of reproduction. A retrograde neural tracer, Fluoro-Gold (FG), was infused into the right side of these regions in ovariectomized rats and the numbers of FG and/or 5-HT immunopositive cells in the right and left sides of the raphe nuclei were counted. It was found that the POA and VMH received more 5-HT projections than the LS from the DR and MR. In the subdivisions of the DR, 70% of all 5-HT projections from the DR to these 3 areas originated from the DRL. Furthermore, ipsilateral projections from the DR to the POA and VMH but not to the LS were dominant, compared to the contralateral projections. A right-left difference was not seen among the MR 5-HT projections. Thus, laterality of the projections is thought to be strong in the 5-HT clusters located far from the midline of the midbrain raphe nuclei.