Abstract The effect of neonatal masseteric nerve transection on primary proprioceptors was examined in the mesencephalic trigeminal tract nucleus (Mes5) of the rat. At 72 h to 21 days after the injury, the number of Mes5 neurons decreased on the side ipsilateral to the transection. The means ± SD of percentage proportion of ipsilateral/contralateral neurons at 72 h and 21 days were 69.9 ± 7.5% and 58.2 ± 14.6%, respectively. The application of brain-derived neurotrophic factor to the proximal stump of the masseteric nerve delayed the loss of Mes5 neurons at 72 h after the injury; the mean numbers ± SD of ipsilateral and contralateral Mes5 neurons in injured animals with BDNF application was 553.6 ± 61.9 and 558.4 ± 55.3, respectively. Saline application had no effect on the injury-induced loss of Mes5 neurons; i.e., the mean numbers ± SD of ipsilateral and contralateral Mes5 neurons were 367.3 ± 72.5 and 543 ± 33.5, respectively. These findings indicate that trigeminal primary proprioceptors are sensitive to the neonatal injury. The survival of proprioceptors during early postnatal period is probably dependent upon brain-derived neurotrophic factor in the trigeminal nervous system.