ABSTRACT Foot type has been associated with pain, injury, and altered gait mechanics. Morphological variations in foot bones due to foot type variation may impact surgical and therapeutic treatments. The purpose of this study was to utilize principal component analysis (PCA) to determine how morphology of the hind‐ and midfoot bones differs among foot types and sex. The calcaneus, talus, navicular, and cuboid were segmented using previously obtained computed tomography (CT) scans and converted to surface models. The CTs were sorted into four foot types—cavus, neutrally aligned, asymptomatic planus, and symptomatic planus. Morphometric shape analysis software (Geomorph) was used to perform a PCA to determine which components varied between foot types and between sexes. The calcaneus showed planus feet of both types to have calcanei that have decreased height and increased length compared to neutrally aligned feet. The talus demonstrated increased posterior mass for cavus feet compared to neutrally aligned feet. For the navicular, symptomatic planus had a more posteriorly positioned tuberosity and were wider than asymptomatic planus feet. The cuboid did not exhibit any differences between foot types. Sex differences, found only at the talus and navicular, were subtle. PCA is an objective technique that helped elucidate differences in bone morphology between foot types and sex without needing to determine the features of interest before comparing groups. Understanding these variations can help inform diagnosis of foot pathologies and surgical protocols as well as improve computer models of the foot. Published 2018. This article is a U.S. Government work and is in the public domain in the USA. J Orthop Res 9999:1–16, 2019. The purpose of this study was to utilize principal component analysis to determine how morphology of the hind‐ and midfoot bones differs due to foot types or sex. Computed tomography scans of cavus, neutrally aligned, asymptomatic planus, and symptomatic planus feet were used for analysis. Morphometric shape analysis elucidated differences in bone morphology among foot types for the calcaneus, talus, and navicular as well as sex‐based differences for the talus. No differences were seen for the cuboid.