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Conclusions: Intraoperative computed tomography (iCT)-guided cochlear implantation is practical and effective for correct electrode placement in the cochlea of patients with congenital inner ear and/or complex middle ear malformation. Objectives: The operation in patients with inner ear and/or complex middle ear malformation including abnormal facial nerve course is difficult. This study evaluated the efficacy of cochlear implantation under the guidance of iCT to insure correct electrode placement. Methods: This was a prospective interventional case series. Ten patients with severe to profound sensorineural hearing loss due to ear malformations were enrolled, and iCT was used to confirm the right placement of electrodes. Results: Intraoperative CT was performed three times in one patient, twice in two, and once in the others. Interruption of the surgical process for each iCT until resumption of surgery was 9.64 ± 0.63 min. iCT revealed incorrectly positioned cochlear implants in two patients, which were immediately corrected. There were no reoperations due to misplacement of electrodes. iCT helped locate the cochlea in the middle ear of one patient with an abnormal facial nerve course. The overall intervention rate based on iCT findings was 30%. Level of evidence: level 4. [ABSTRACT FROM AUTHOR]