The lateral habenular nucleus (LHb) projects to the dorsal raphe nucleus (DRN) and ventral tegmental area (VTA). Prior studies have reported that the medial division of the LHb (LHb-m) mainly projects to the DRN, while the LHb mainly projects to the ipsilateral VTA; however, due to only a few studies of projection ratio analysis, the degree of projection of minor and major pathways remains unclear, and the potential significance of minor pathways may be overlooked. After injecting the retrograde tracer into the mice DRN, the proportion of labeled neurons was 63.50% in the LHb-m and 36.50% in the lateral division of the LHb (LHb-l). The proportion distributions of labeled neurons were 26.90% in the anterior LHb-m and 73.10% in the posterior LHb-m. When the retrograde tracer was injected into the VTA, the percentage of labeled neurons was 64.85% in the ipsilateral LHb and 35.15% in the contralateral LHb. The number of cells projecting from anterior and posterior ipsilateral LHb-m to the VTA varied among the individual injection sites. Our quantitative analysis with multiple subjects showed that the projections from LHb-l to DRN and from LHb to contralateral VTA were indeed minor pathways, however, they were substantial. These results provide an anatomical basis for the potential importance of minor pathways projected from the LHb to the VTA and DRN and for the difference in the densities of neurons projecting from the anterior and posterior LHb-m to the DRN.