The sternocleidomastoid and trapezius muscles of the rat, which are innervated by the spinal accessory nerve (SAN) and cervical spinal nerve (CSN), consist of five smaller muscles: the sternomastoid, cleidomastoid, clavotrapezius, acromiotrapezius, and spinotrapezius. In this study, the location of cell somata of the motoneurons supplying each of these smaller muscles and the peripheral course of their axons have been studied by means of the horseradish peroxidase retrograde axonal transport technique (the HRP method) in combination with cutting of the SAN. The sternocleidomastoid and trapezius motoneurons formed three cell columns, column-M, -L, and -5, in the ipsilateral ventral horn of the cervical spinal cord. Column-M and -L extend longitudinally in the medial nucleus of C1 and C2 and in the ventrolateral nucleus from the middle of C2 to the middle of C6, respectively. These columns consist of the motoneurons whose axons pass through the SAN and they merge in the caudal C2 to constitute the spinal accessory nucleus. Column-5, which consists of the motoneurons passing through the CSN, extends longitudinally from C3 to C5 close to column-L in the ventrolateral nucleus. Motoneurons supplying the sternomastoid, cleidomastoid, clavotrapezius, acromiotrapezius, and spinotrapezius muscles showed a rostrocaudal somatotopic distribution in the spinal accessory nucleus and in column-5 in this order, though the sternomastoid motoneurons were not found in column-5.