Inner ear malformations (IEMs) may result in differences in outcomes of cochlear implant user. These differences could be observed in both behavioral and objective tests. eCAP is the most common used objective test in cochlear implants and have different presence rate in cochlear implant users with and without IEMs. This study aims to evaluate eCAP results from CI user with and without IEMs through different recoding methods; amplitude growth function, spreads of excitation and refractory recovery. There were 42 CI users (20 IEM&22 normal) above five-years old and with at least one year experience. Three different eCAP measurement was conducted at several intracochlear electrodes. Presence rate, threshold levels and amplitude were compared between groups. For Amplitude growth function measurement, when the percentage of detected eCAP thresholds was analyzed between groups, there was a significant difference only for basal electrode and no significant difference for apical and middle electrodes. Similarly, the presence rate of RecF-eCAP for both groups were in a downward trend from apical to basal. However, there was no significant difference in AGF-eCAP and RecF-eCAP amplitudes between groups for the cochlea's apical, middle and basal region. Although the presence rate of SOE-eCAP was lower for IEM group, there was no significant difference in ECAP amplitudes for all maskers. It could be inferred that even though the observable eCAP rate differed between these two groups when the observable eCAP was recorded, the IEM group produced eCAP with similar amplitudes to normal cochlea group.