We conducted a prospective study to investigate the abnormalities of the facial nerve canal in patients with congenital aural atresia by computed tomography (CT). Our study population was made up of 99 patients-68 males and 31 females, aged 6 to 22 years (mean: 13.5)-who had unilateral congenital aural atresia without any inner ear malformations. We compared our findings in these patients with those in 50 controls-33 males and 17 females, aged 5 to 22 years (mean: 15.0)-who had normal ears. We classified the congenital aural atresia patients into three groups (A, B, and C) according to their Jahrsdoerfer grading scale score (≥8; 6 or 7; and ≤5, respectively). The course of the facial nerve canal in both the controls and the study patients was determined by temporal bone CT with multiplanar reconstruction. The distances from different parts of the facial nerve canal to surrounding structures were also measured. The course of the facial nerve canal in the normal ears did not vary much, and there were no statistically significant differences according to head side and sex. In groups B and C, the tympanic segment, mastoid segment, and angle of the second genu of the facial nerve canal were all significantly smaller than those of the controls (p < 0.01 in all cases). Statistically, the tympanic segment of the facial nerve canal in patients with congenital aural atresia was downwardly displaced. The mastoid segment of the facial nerve canal in these patients was more anterior than that of the controls. We conclude that congenital aural atresia is often accompanied by abnormalities of the facial nerve canal, especially in the tympanic segment, the mastoid segment, and the second genu. We found that the lower the Jahrsdoerfer score was, the shorter the tympanic segment was and the more forward the mastoid segment was.