Background. The complex deformities in cavovarus feet may be difficult to assess and understand. Weight-bearing CT (WBCT) is increasingly used to evaluate complex deformities. However, the bone axes may be difficult to calculate in the setting of severe deformity. Computer-assisted 3D-axis calculation is a novel approach that may allow for more accurate assessment of foot alignment / deformity. The aim of this study was to assess differences in measurements done manually on 2D slices of WBCT versus 3D computer models in normal and cavus feet. Methods. We retrospectively analyzed WBCT scans from 16 normal and 16 cavus feet in patients with Charcot-Marie Tooth. Eight measurements were assessed: Talus-1. st. metatarsal angle (axial plane), Forefoot arch angle (coronal plane), and Meary's angle, calcaneal pitch, cuneiform to floor, cuneiform to skin, navicular to floor and navicular to skin distance (sagittal plane). 2D measurements were performed manually and 3D measurements were performed using specialised software (BoneLogic, DISIOR). Results. There was no significant difference in the measured variables (2D manual versus 3D automated) in normal feet. In the cavus group, 3D assessment calculated increased values for the sagittal angles: Meary's 7.3 degrees greater (p = 0.004), calcaneal pitch 2.4 degrees greater (p = 0.011)), and lower values for the axial talus-1. st. MT angle, 10.6 degrees less (p = 0.001). Conclusion. There were no significant differences in the normal group. This suggests 3D automated techniques can reliably assess the alignment of bony axes. However, the 3D axis calculations suggest there may be greater sagittal and lesser axial deformity in cavus feet than measured by 2D techniques. This discrepancy may be on account of the rotation seen in cavovarus feet, which may not be readily assessed manually. 3D automated measurements may therefore have a role in better assessing and classifying the cavus foot which may ultimately help inform treatment algorithms