Hypothesis: The presence of bony inner ear malformations may associate with a number of anatomical abnormalities affecting the middle ear structures. Those malformations may create pitfalls and complications for cochlear implantation. Background: Inner ear malformations associate with varying degrees of hearing loss, and frequently require cochlear implantation for hearing rehabilitation. Therefore, the abnormalities affecting the middle- and inner-ear structures may increase the risk of surgical complications. Methods: We examined 38 human temporal bones from donors with bony inner ear malformations. Using light microscopy, we analyzed the presence of abnormalities in the structures of the middle- and inner-ear. Results: Our collection comprises of 38 specimens with inner-ear malformations (cochlear aplasia, n = 3; cochlear hypoplasia, n = 30; incomplete partition, n = 3; isolated vestibular malformation, n = 2). The anatomy of the middle ear was abnormal in most temporal bones with cochlear aplasia, cochlear hypoplasia, and incomplete partition type I (40%–100%). Some of those abnormalities (hypoplastic or obliterated mastoid, 55.2%; aplastic or obliterated round window, 71.0%; aberrant course of the facial nerve, 36.8%) may hinder the access to the round window using the conventional facial recess approach for cochlear implantation. The cochlear nerve and associated bony structures (internal auditory canal and bony canal for cochlear nerve) were normal in 71.0% of all temporal bones with inner ear malformations. Conclusion: Each different type of malformation may create specific surgical challenges to surgeons. Comprehensive preoperative imaging is fundamental toward the surgical success of cochlear implants in patients with malformations. Alternatives to circumvent those middle- and inner-ear abnormalities and potential complications are further discussed.