Hypothesis Unilateral congenital conductive hearing impairment in ear canal atresia leads to atrophy of the gray matter of the contralateral primary auditory cortex or changes in asymmetry pattern if left untreated in childhood. Background Unilateral ear canal atresia with associated severe conductive hearing loss results in deteriorated sound localization and difficulties in understanding of speech in a noisy environment. Cortical atrophy in the Heschl's gyrus has been reported in acquired sensorineural hearing loss but has not been studied in unilateral conductive hearing loss. Methods We obtained T1w and T2w FLAIR MRI data from 17 subjects with unilateral congenital ear canal atresia and 17 matched controls. Gray matter volume and thickness were measured in the Heschl's gyrus using Freesurfer. Results In unilateral congenital ear canal atresia, Heschl's gyrus exhibited cortical thickness asymmetry (right thicker than left, corrected p = 0.0012, mean difference 0.25 mm), while controls had symmetric findings. Gray matter volume and total thickness did not differ from controls with normal hearing. Conclusion We observed cortical thickness asymmetry in congenital unilateral ear canal atresia but no evidence of contralateral cortex atrophy. Further research is needed to understand the implications of this asymmetry on central auditory processing deficits.