In this study, the responses of nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d) and neuronal nitric oxide synthase (nNOS) activities were quantitatively analyzed at different times in both ipsilateral and contralateral sides of trigeminal nuclei, after unilateral trigeminal muscle nerve transection, in Sprague Dawley rats. In the control animals, both NADPH-d- and nNOS-positive neurons were constitutively distributed in the rostrolateral solitary tract nucleus, dorsomedial part of trigeminal nucleus oralis (Vo/Sn), and superficial layers (VcI/II) of the trigeminal nucleus caudalis (Vc). NADPH-d-positive neurons appeared in the trigeminal mesencephalic nucleus ipsilaterally at 5 days (mean +/- SEM: 30.5 +/- 5.6) and were maintained until 8 weeks (33 +/- 10.6) after the denervation. In the trigeminal motor nucleus, NADPH-d-positive neurons appeared transiently and bilaterally, peaking at 1 week (663.5 +/- 156.2, ipsilateral side; 687.5 +/- 118.6, contralateral side) after unilateral denervation of the masseteric nerve. In both Vo/Sn and Vc, the number of NADPH-d-positive neurons in the control animals showed a decrease at 3 days but significantly increased from 5 days to 1 week and gradually fell to the control values by 8 weeks after the denervation. There were no significant differences observed between the two sides in either Vo/Sn or Vc. nNOS-positive neurons were similarly distributed and the numbers of labeled neurons were similar to those of NADPH-d-positive neurons after the denervation, although the changes were delayed by approximately 1 week. In conclusion, after unilateral nerve transection, the peak NADPH-d activity occurs 1 week prior to nNOS activity.