Electrophysiological and lesion studies in rodents have shown that there is a functional dissociation between the dorsal and ventral hippocampus with regard to their involvement in spatial cognition, emotion, and stress. In this study we examined the difference of the disynaptic inputs to the dorsal and ventral dentate gyrus (DG) in the rat by using recombinant rabies virus vectors. Rabies virus vectors can infect neurons transsynaptically in a retrograde direction and label infected neurons by the expression of fluorescent proteins. By using these viral vectors, we identified the brain areas that project to the DG disynaptically, such as the piriform and medial prefrontal cortices, the endopiriform nucleus, the claustrum, the cortical amygdala, the medial raphe nucleus, the medial habenular nucleus, the interpeduncular nucleus, and the lateral septum. In order to precisely examine the differences of the multisynaptic inputs to the dorsal and ventral DG, we used a dual transsynaptic tracing method that can separately label two distinct neural circuits in the same experiment. In line with previous anatomical studies using conventional chemical tracers, topographical projection patterns to the dorsal and ventral DG were observed in the regions known to project to the DG directly (entorhinal cortex, medial septum, diagonal band, supramammillary nucleus). Topographical distribution of labeled neurons were also observed in most of the disynaptically labeled regions. These data indicate that the cortical and subcortical inputs to the dorsal and ventral DG are conveyed through parallel disynaptic pathways. This difference in the disynaptic inputs to the dorsal and ventral DG is likely to contribute to the functional differentiation of the hippocampus along the dorsoventral axis.