Loss of cochlear hair cells in the rat initiates degenerative change within the primary auditory neurons (ANs) of the cochlea. These degenerative changes include loss of peripheral processes, demyelination and ultimately cell death. This pathology will affect the biophysical processes involved in action potential generation and propagation to an electrical stimulus via a cochlear implant. We measured the response properties of ANs, with particular reference to their refractory behaviour, in normal, short- (9 weeks) and long-term (> 52 weeks) deafened rats. AN loss was moderate in the short-term and severe in the long-term deafened animals. AN activity was elicited using a brief electrical stimulus delivered via a bipolar electrode array implanted into the cochlea. The general response properties of ANs recorded from deafened cochleae were similar to those observed in normal cochleae, i.e. a monotonic increase in the probability of firing and a decrease in response latency and temporal jitter with increasing stimulus intensity. However, the absolute refractory period was significantly prolonged in animals deaf for > 12 months (P = 0.0026). Deafened animals also exhibited a highly significant increase in threshold compared with normal controls (P < 0.001). These functional changes have implications for recipients of cochlear implants and potential therapies directed toward halting or reversing AN pathology.