Planus and cavus foot types have been associated with an increased risk of pain and disability. Improving our understanding of the geometric differences between bones in different foot types may provide insights into injury risk profiles and have implications for the design of musculoskeletal and finite element models. In this study we performed a geometric morphometric analysis on the geometry of metatarsal bones from 65 feet, segmented from computed tomography scans. These were categorized into four foot types: pes cavus, neutrally aligned, asymptomatic pes planus, and symptomatic pes planus. Generalized Procrustes analysis followed by permutation tests were used to determine significant shape differences associated with foot type and sex, and principal component analysis used to find the modes of variation for each metatarsal. Significant shape differences were found between foot types for all metatarsals (p<0.01), most notably in the case of the second metatarsal which showed significant pairwise differences across all foot types. Analysis of the principal components of variation showed pes cavus bones to have reduced cross-sectional areas in the sagittal and frontal planes. The first and fourth metatarsals were found to have significant sex-based differences, with first metatarsals from females shown to have reduced width, and fourth metatarsals from females shown to have reduced frontal and sagittal plane cross sectional areas. Overall, these findings suggest that metatarsal bones have distinct morphological characteristics that are associated with foot type and sex, with implications for our understanding of anatomy and numerical modelling of the foot.