Most cochlear implants (CIs) stimulate the auditory nerve with trains of symmetric biphasic pulses consisting of two phases of opposite polarity. Animal and human studies have shown that both polarities can elicit neural responses. In human CI listeners, studies have shown that at suprathreshold levels, the anodic phase is more effective than the cathodic phase. In contrast, animal studies usually show the opposite trend. Although the reason for this discrepancy still remains unclear, computational modelling results have proposed that the degeneration of the peripheral processes of the neurons could lead to a higher efficiency of anodic stimulation. We tested this hypothesis in ten guinea pigs who were deafened with an injection of sysomycin and implanted with a single ball electrode inserted in the first turn of the cochlea. Animals were tested at regular intervals between 1 week after deafening and up to 1 year for some of them. Our hypothesis was that if the effect of polarity is determined by the presence or absence of peripheral processes, the difference in polarity efficiency should change over time because of a progressive neural degeneration. Stimuli consisted of charge-balanced symmetric and asymmetric pulses allowing us to observe the response to each polarity individually. For all stimuli, the inferior colliculus evoked potential was measured. Results show that the cathodic phase was more effective than the anodic phase and that this remained so even several months after deafening. This suggests that neural degeneration cannot entirely account for the higher efficiency of anodic stimulation observed in human CI listeners.