Background: In patients with congenital sensorineural hearing loss (SNHL), a computed tomography (CT) scan of the temporal bone identifies inner ear malformations in approximately 25%, whereas the inner ear is grossly normal to visual inspection in the remaining 75% of the patients. In the latter group, the hearing loss is often attributed to radiologically undetectable abnormalities of the membranous labyrinth. However, subtle bony malformations may be missed because visual inspection alone is insensitive for detection. Objective: To test the hypothesis that there are subtle bony abnormalities of the inner ear in patients with SNHL who are radiologically deemed to have normal otic bone, using standardized measurements of the inner ear. Study Design: Retrospective review. Methods: Measurements of the cochlea, vestibule, and semicircular canals (SCCs) were made on axial and coronal temporal bone CT scans on 15 patients with normal hearing and 15 patients with congenital SNHL and grossly normal temporal bone CT scans. Student's t‐test was performed to compare the measurements of the two groups. Results: All studies from the SNHL group were deemed normal by visual inspection and standardized measurements (±2 SD from normal). Surprisingly, there were significant differences in the measurements of the cochlea and of the SCCs between patients with and without SHNL (P < .05). Conclusions: As a group, patients with SNHL and a “normal CT scan” have significant differences in the dimensions of the inner ear. This suggests that these patients have disturbed morphogenesis of both membranous and bony labyrinth. This novel observation has important implications for understanding the etiology of SNHL.