Objectives: To report histopathologic and anatomic features in human temporal bones with inner ear malformations and their potential impact in cochlear implantation. Methods: From the human temporal bone collection of the University of Minnesota, we selected specimens from donors who had inner ear malformations, which were categorized as proposed by Sennaroglu and Bajin. We analyzed morphologic aspects, middle ear abnormalities, internal architecture, and neural structures of the inner ear. Results: We found 30 human temporal bones from 16 donors who had inner ear malformations. Inner ear malformations were associated with a number of syndromes (trisomy of 21, CHARGE, first and second branchial arch syndrome, C/D chromosome translocation). Most specimens (n = 23; 76.6%) were classified as cochlear hypoplasia type 3. Other malformations were cochlear hypoplasia type 2 (n = 2), incomplete partition type II (n = 2), and cochlear aplasia (n = 3). Most bones with malformations (except cochlear aplasia) had normal or near-normal vestibulocochlear nerves and spiral ganglion neural cells. However, most bones had abnormalities affecting the middle ear cavity, mastoid, and facial nerve that could hinder access to the round window through facial recess approach. Conclusions: Considering that patients with inner ear malformations frequently have profound hearing loss, our histologic findings suggest that patients with cochlear hypoplasia type 2, type 3, and incomplete partition type II have normal or near-normal neural structures and may benefit from cochlear implantation as a first treatment strategy. However, the abnormalities observed suggest potential anatomic pitfalls that could restrict correct placement of the electrode or increase the risks of surgical complications.