Using nitric oxide synthase (NOS) and glutamate receptor subunit 1 (GluR1) immunohistochemistry, the present study demonstrated changes in the expression of NOS and GluR1 in the hypoglossal (HN) and dorsal vagal nucleus (DVN) after neurectomy. Two and 7 days after sectioning the left hypoglossal nerve, NOS expression was seen in a few neurons but GluR1 immunoreactivity was drastically reduced in the ipsilateral HN. The upregulation of NOS immunoreactivity in the HN appeared to peak at 14 days postoperation (dpo). At this period, however, the GluR1 immunoreactivity almost completely disappeared. Twenty-one, 35 and 56 days after neurectomy, NOS immunoreactivity was still expressed in the ipsilateral HN; at the same time, GluR1 immunoreactivity reappeared in a few neurons of the nucleus. Ninety days after operation, NOS immunoreactivity completely disappeared on the operated side of the nucleus, but GluR1 immunoreactivity was re-expressed in many hypoglossal neurons. The number of such neurons was obviously less than that on the unoperated side. After sectioning the left vagus nerve in the same animals, the expression of NOS immunoreactivity in the ipsilateral DVN resembled that in the HN. On the unoperated side, NOS immunoreactivity was demonstrated in some neurons in the DVN, like that in the normal. In both normal and operated rats, only a few neurons expressed GluR1 immunoreactive products on both the operated and unoperated sides of the DVN. Combining with previous results on protein synthesis observed at 14 dpo, the present investigation suggested that in the early stages after neurectomy, the expression of NOS immunoreactivity and loss of GluR1 expression in the HN may indicate the organism's double protective mechanism. Lastly, the reappearance of GluR1 in the same nucleus from 21 to 90 days after operation may reflect functional recovery of the hypoglossal neurons.