Transganglionic transport of horseradish peroxidase-wheat germ agglutinin conjugate was used to study the central projection of primary afferent neurons innervating facial and intraoral structures. The examined primary neurons innervating the facial structures were those comprising the frontal and zygomaticofacial nerves and those innervating the cornea, while the primary neurons innervating the intraoral structures included those innervating the mandibular incisor and molar tooth pulps and those comprising the palatine nerve. The primary afferents innervating the facial structures project to the lateral or ventral parts of the trigeminal principal, oral and interpolar subnuclei, and to the rostral cervical spinal dorsal horn across laminae I through V, with a greater proportion being directed to the spinal dorsal horn. The primary afferents innervating the intraoral structures terminate in the dorsomedial subdivisions of the trigeminal principal, oral and interpolar subnuclei, and in laminae I, II, and V of the medial medullary dorsal horn, with a much denser projection being distributed to the rostral subnuclei. In addition to the above brain stem trigeminal sensory nuclear complex, they project to the supratrigeminal nucleus, caudal solitary tract nucleus, and paratrigeminal nucleus. These observations agree with previously reported data that the central projection of trigeminal nerve is organized in different manners for the facial and intraoral structures. Furthermore, the present findings in conjunction with our previous studies clarify that the central projection of primary afferents from the facial skin is organized in a clear somatotopic fashion and that the terminal fields of primary afferents from the intraoral structures extensively overlap in the brain stem trigeminal nuclear complex particularly in its rostral subdivisions. The central mechanism of trigeminal nociception is discussed with particular respect to its difference between the facial and intraoral structures.