This case study presents the neuroradiological findings of two deaf children with CHARGE syndrome and oculo-auriculo-vertebral spectrum disease. Both patients had rare combinations of ear and auditory nerve anomalies associated with a high risk of intra- and postoperative complications during cochlear implantation (CI) and poor results. However, CI was carried out with favorable results in terms of hearing and speech development. When determining indications for CI in children with complex anomalies, it is necessary to assess the state of all ear structures in computed tomography of the temporal bones and MR (3 Tesla) images. The most critical is the state of the following structures: cochlea—modiolus—cochlear aperture—diameter of the internal auditory canal—the presence and condition of the auditory nerve. In the presence of a normal or dysplastic cochlea, a hypoplastic auditory nerve is not a contraindication for CI. In this situation, the presence of a modiolus and at least partially open cochlear aperture are prognostically favorable. In the presence of a large or small common cavity, an undivided vestibulocochlear nerve is not considered a contraindication for CI. Such a combination—a common cavity and an undivided vestibulocochlear nerve—is a prognostically quite favorable option.