Recent advances in the study of pain have revealed somatotopic- and modality-dependent processing and the integration of nociceptive signals in the brain and spinal cord. This review summarizes the uniqueness of the trigeminal sensory nucleus (TSN) in structure and function as it relates to orofacial pain control. The oral nociceptive signal is primarily processed in the rostral TSN above the obex, the nucleus principalis (Vp), and the subnuclei oralis (SpVo) and interpolaris (SpVi), while secondarily processed in the subnucleus caudalis (SpVc). In contrast, the facial nociceptive signal is primarily processed in the SpVc. The neurons projecting to the thalamus are localized mostly in the Vp, moderately in the SpVi, and modestly in the ventrolateral SpVo and the SpVc. Orofacial sensory inputs are modulated in many different ways: by interneurons in the TSN proper, through reciprocal connection between the TSN and rostral ventromedial medulla, and by the cerebral cortex. A wide variety of neuroactive substances, including substance P, γ-aminobutyric acid, serotonin and nitric oxide (NO) could be involved in the modulatory functions of these curcuits. The earliest expression of NO synthase (NOS) in the developing rat brain is observed in a discrete neuronal population in the SpVo at embryonic day 15. NOS expression in the SpVc is late at postnatal day 10. The neurons receiving intraoral signals are intimately related with the sensorimotor reflexive function through the SpVo. In summary, a better understanding of the trigeminal sensory system - which differs from the spinal system - will help to find potential therapeutic targets and lend to developing new analgesics for orofacial-specific pain with high efficacy and fewer side effects.