The neuronal nuclei (NeuN) antibody, which binds to a poorly characterized antigen/antigens, is increasingly being used in several areas of study as a specific marker to identify neuronal populations. Despite the increasing reliance on NeuN as a panneuronal marker, changes of NeuN expression following axonal injury have not yet been examined. In the present study, NeuN immunoreactivity was analyzed in adult rodent facial motoneurons [peripheral nervous system (PNS) model] following nerve resection or crush and in rubrospinal neurons [central nervous system (CNS) model] after lesion of the dorsal lateral funiculus at the cervical level of the spinal cord. Peripheral nerve resection in the rat and mouse resulted in an almost complete loss of NeuN immunoreactivity in facial motoneurons by 3 days postinjury and remained absent at 28 days post-resection despite the survival of the neurons as evidenced by neuronal tracing. These results were confirmed with Western blot. In the peripheral nerve crush model of injury, there was an initial decline in NeuN immunoreactivity in facial motoneurons, but unlike the resection model, NeuN immunoreactivity began to return within 7 days postinjury and returned to the uninjured level of expression by 28 days. In contrast, axotomy in the CNS model resulted in little decline in NeuN immunoreactivity in the rubrospinal neurons, even after 28 days postaxotomy. These results indicate that NeuN expression in response to axonal injury is different in separate neuronal populations (PNS and CNS), and that care must be taken when addressing cell survival based on NeuN staining alone.