Endomorphin-2-immunoreactive (EM2-IR) fibers and terminals are densely present in the medullary dorsal horn (MDH) and are key factors in regulating central nociceptive processing. However, the origins of these EM2-IR fibers and terminals remain elusive. It was hypothesized that there were at least three possible origins of the EM2-IR fibers and terminals in the MDH: intrinsic dorsal horn neurons, primary afferent fibers, and projection fibers from higher parts of the brain. Different kinds of measures were employed in the current study to elucidate this hypothesis. After intracerebral ventricle administration of colchicine, no EM2-IR neuronal cell bodies were detected in the MDH, suggesting that there was no intrinsic EM2-IR dorsal horn neuron. Disruption of bilateral primary afferents (exposed to the primary afferent neurotoxin, capsaicin) decreased bilateral EM2 expression but did not eliminate it. Transection of the trigeminal nerve sensory root significantly decreased EM2 expression on the ipsilateral but not on the contralateral MDH. After injecting FluoroGold (FG) into the MDH, FG retrogradely labeled some EM2-IR neurons in the bilateral hypothalamus and nucleus tractus solitarii (NTS), and some of the FG retrogradely labeled neurons in the ipsilateral trigeminal ganglion also showed EM2-immunoreactivities. These results indicate that EM2-IR fibers and terminals in the MDH come not only from ipsilateral primary trigeminal afferents but also from bilateral fibers from the hypothalamus and NTS.