A prospective case-control study was performed comparing axial and coronal CT scan images of 11 patients (14 ankles) with chronic lateral instability and 12 controls. Scans were performed in a standardized fashion to simulate weight-bearing. Nine measurements to evaluate the alignment of the hindfoot and forefoot were made on two occasions by two observers. The blinded images were read in order of assigned random number. The angle between the calcaneus and the vertical plane showed a statistically significant difference between patients (6.4 +/- 4 degrees varus from vertical) and controls (2.7 +/- 5 degrees) using unpaired ANOVA (p < 0.01). Intra-observer (R2 = 0.49 +/- 0.19) and interobserver (R2 = 0.71 +/- 0.13) variation showed moderate reliability across all measurements. This study demonstrates a method to evaluate hindfoot varus on CT scan. Many factors have been studied (e.g., proprioception) as the cause for recurrent instability, and this is the first time, to our knowledge, that an anatomic cause has been demonstrated. Although calcaneal osteotomy is clearly not indicated routinely, it may have a role in correcting extreme varus, which may contribute to failed ligament reconstruction in patients with ankle instability.