The objective of this study is to use standardized measurements of the inner ear to see whether there are subtle bony malformations in children with congenital sensorineural hearing loss (SNHL) whose temporal bone computed tomography (CT) are grossly normal. The study includes 45 ears with congenital SNHL and grossly normal temporal bone CT scans and 45 ears with normal inner ear structures and normal hearing. Standardized measurements of the inner ear structures were made on axial temporal bone CT scans. Student's t test was performed to compare the measurements of the two groups. There were significant differences in the measurements of the bony island width of the superior semicircular canal, bony island width of the lateral semicircular canal and maximal height of cochlea between two groups (P < 0.05). In conclusion, standardized measurements of bony labyrinth of inner ear on temporal bone CT can identify subtle abnormalities of inner ear in patients with congenital SNHL having grossly normal radiological images.