Orofacial injury activates two distinct regions in the spinal trigeminal complex, the subnuclei interpolaris/caudalis (Vi/Vc) transition zone and the laminated Vc, or medullary dorsal horn (MDH). Studies suggest that the Vi/Vc transition zone plays an important role in processing orofacial deep input. To test this hypothesis, we employed a double-tracing strategy to compare central projections of primary afferent neurons that innervate the masseter muscle and the overlying skin. Different tracers were injected either centrally (Fluoro-Gold: ventral Vi/Vc, or MDH) or peripherally (wheat germ agglutinin-conjugated horseradish peroxidase or cholera toxin B: masseter or overlying skin) in the same rat. Trigeminal ganglion tissue sections were processed for single or double immunohistochemistry. The double labeling of ganglion neurons indicates their site of peripheral and central innervations. A population of small to medium-sized neurons was doubly labeled after injections of the tracers into the masseter-Vi/Vc, masseter-MDH, or the skin-MDH. However, only a few double-labeled neurons were occasionally observed after injections of the tracers into the skin-Vi/Vc. Injection of an N-methyl-D-aspartate receptor antagonist, AP-5, into the Vi/Vc and MDH attenuated masseter inflammatory hyperalgesia. In contrast, hyperalgesia after inflammation of the skin overlying the masseter was attenuated by injection of AP-5 into the MDH but not Vi/Vc. These results indicate that while both masseter and cutaneous inputs project to the MDH, masseter afferents provide an additional input to the Vi/Vc. These findings provide further evidence to support a role of the trigeminal transition zone in response to orofacial deep injury.