The study was designed to assess the electrically evoked compound action potential (ECAP) responses in children with inner ear malformations compared to children with normal inner ear anatomy. The study included 235 prelingual deaf children who were implanted in cochlear implant unit in King Fahad University hospital-Imam Abdulrahman Bin Faisel University. Subjects were using either Cochlear Nucleus or Medel cochlear implant devices. We had 171 (64.5%) subjects with normal inner ear anatomy and 94 (35.5%) subjects with inner ear malformations (IEMs) and they were classified into 6 groups according to inner ear anatomy. Fourteen subjects (14.9%) subjects had enlarged vestibular aqueduct (EVA), 30 (32%) subjects had Mondini deformity, 25 (26.6%) subjects had incomplete partition type two (IPII), 9 (9.6%) subjects had incomplete partition type one (IPI) and 16 (17%) subjects had hypoplastic cochlea type III or IV. Intraoperative electrically evoked compound action potential (ECAP) responses were analyzed and compared in all subjects. Measurable ECAP responses can be elicited in patients with IEMs in most of the channels. Severe malformations can affect the prevalence of measuring ECAP and getting identifiable waveform morphology. Additionally, increased thresholds and lower slope of AGF was observed in IEMs specially in more severe malformations (e.g. IPI). IPI patients with better word recognition scores tended to show more identifiable ECAP measurements. This could suggest the presence of some correlation between ECAP responses and patients' performance after cochlear implantation.