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Cochlear implants rely on the integrity and correct functioning of auditory nerves. However, after sensorineural hearing loss there is a well-characterised degeneration of auditory nerves. One proposed mechanism of this degeneration is a reduction in the levels of neurotrophins, which are naturally occurring proteins that aid the growth and maintenance of neurons. Neurotrophin application to the cochlea of animals prevent morphological degeneration of the auditory nerves after deafness, making it a promising treatment for improving cochlear implant outcomes. The current study examined the effects of two major neurotrophins present in the cochlea, brain-derived neurotrophic factor and neurotrophic factor-3, on the function of individual auditory nerve fibres to cochlear implant stimulation. Guinea pigs were ototoxically deafened and then divided into groups that received treatment for four weeks with either brain derived neurotrophic factor, neurotrophin factor-3 or Ringer's solution as a control. Treatments were administered one week after deafening and delivered to the left cochlea through a combined cannula-electrode array that was attached to a mini-osmotic pump. Additional control groups included guinea pigs deafened for five weeks and an acutely deafened group. At the end of the treatment period responses of individual auditory nerve fibres to acute electrical stimulation of the cochlea at rates from 200-5000 pulses per second were recorded. Both brain derived neurotrophic factor and neurotrophin-3 treatment generally normalized the reduction in spike latency of auditory nerve fibres observed after deafness. BDNF significantly reduced thresholds compared to all control groups, while NT-3 did not. Both BDNF and NT-3 increased the first-spike dynamic range compared to untreated groups. These results were largely similar regardless of the stimulus rate used. These results suggest that neurotrophin treatment of the cochlea after deafness appears to preserve the latency of auditory nerve fibres, but may alter the response threshold and dynamic range. Further investigations are required to determine if neurotrophins are likely to preserve or improve auditory nerve function when used with a cochlear implant. [ABSTRACT FROM AUTHOR]