Neuron-specific enolase (NSE) is a glycolytic isoenzyme which is located in central and peripheral neurons and neuroendocrine cells. Another enolase isoenzyme, non-neuronal enolase (NNE), occurs in glial cells. The purpose of this study was to follow any changes in NSE and/or NNE in cranial motor neurons after separation of their cell bodies from their axon terminals. One hypoglossal nerve in the rat and the cynomolgus monkey was thus crushed or cut and, after a given period, the brains were perfusion fixed. Immunocytochemistry, using anti-rat NSE and NNE or anti-human NSE and NNE, was performed on Vibratome-sectioned specimens of the hypoglossal nuclei. In the rat, NSE immunostaining decreased in the affected neurons 2 to 10 days following axonal injury. The change was greatest on the 10th day. Twenty days following nerve crush. NSE staining began to recover on the operated side and by the 45th day had returned to normal levels. NSE changes in the monkey were similar to those in the rat. In rats, where the nerve was cut and the proximal stump was translocated to a normally innervated muscle to inhibit re-formation of synaptic contacts, the NSE remained low for 60 days after nerve injury. As NSE levels fell during degeneration, there was a slight increase in NNE in some of the monkey specimens but not in others; the NNE alterations were, therefore, equivocal. The results demonstrate that the content of NSE in neurons serves as a molecular marker of axon injury, regeneration, and target reinnervation.