Previous studies have shown that residual acoustic hearing supplements cochlear implant function to improve speech recognition in noise as well as perception of music. The current study had two primary objectives. First, we sought to determine how cochlear implantation and electrical stimulation over a time period of 14 to 21 months influence cochlear structures such as hair cells and spiral ganglion neurons. Second, we sought to investigate whether the structures that provide acoustic hearing also affect the perception of electrical stimulation. We compared psychophysical responses to cochlear implant stimulation in two groups of adult guinea pigs. Group I (11 animals) received a cochlear implant in a previously untreated ear, while group II (ten animals) received a cochlear implant in an ear that had been previously infused with neomycin to destroy hearing. Psychophysical thresholds were measured in response to pulse-train and sinusoidal stimuli. Histological analysis of all group I animals and a subset of group II animals was performed. Nine of the 11 group I animals showed survival of the organ of Corti and spiral ganglion neurons adjacent to the electrode array. All group I animals showed survival of these elements in regions apical to the electrode array. Group II animals that were examined histologically showed complete loss of the organ of Corti in regions adjacent and apical to the electrode array and severe spiral ganglion neuron loss, consistent with previous reports for neomycin-treated ears. Behaviorally, group II animals had significantly lower thresholds than group I animals in response to 100 Hz sinusoidal stimuli. However, group I animals had significantly lower thresholds than group II animals in response to pulse-train stimuli (0.02 ms/phase; 156 to 5,000 pps). Additionally, the two groups showed distinct threshold versus pulse rate functions. We hypothesize that the differences in detection thresholds between groups are caused by the electrical activation of the hair cells in group I animals and/or differences between groups in the condition of the spiral ganglion neurons.