Although virtually all of serotonin (5-HT) neurons in the midbrain raphe nuclei of rats are known to express vesicular glutamate transporter 3 (VGLUT3), VGLUT3-positive 5-HT fibers have been identified only in the cerebral cortex and hippocampus. Thus, our understanding of forebrain sites where 5-HT-glutamate interaction may be potentially managed by such possible glutamatergic 5-HT fibers themselves, is still largely fragmentary from a morphological point of view. To address this issue, we analyzed the rat forebrain by immunohistochemistry and chemical lesion experiment of 5-HT neurons by intracerebroventricular injection of a neurotoxin, 5,7-dihydroxytriptamine. Contrary to expectation, the double-label immunofluorescence staining revealed that the incidence of VGLUT3-positive 5-HT fibers is generally low over the forebrain, demonstrating occasional fibers with one or two double-labeled varicosities. The most extreme example was the nucleus of the lateral olfactory tract (LOT), which seemed to be devoid of double-labeled fibers despite high densities of 5-HT fibers and VGLUT3-positive fibers. In sharp contrast, robust plexuses of VGLUT3-positive 5-HT fibers were found in the dorsal, but not ventral, part of the lateral septum. The lesion experiment carried out to explore whether VGLUT3 exists in 5-HT fibers showed that in lesioned rats VGLUT3-positive fibers almost completely disappear from the septal region but seemed unchanged in the LOT. The present study shows that midbrain raphe-derived 5-HT fibers can be classified into two subtypes depending on co-expression with VGLUT3 staining in the forebrain.