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The understanding of foot and ankle biomechanics is improving as new technology provides more detailed information about the motion of foot and ankle bones with biplane fluoroscopy, as well as the ability to analyze the hindfoot under weightbearing conditions with weightbearing computed tomography. Three-dimensional anatomical coordinate systems are necessary to describe the 3D alignment and kinematics of the foot and ankle. The lack of standard coordinate systems across research study sites can significantly alter experimental data analyses used for pre-surgical evaluation and post-operative outcome assessments. Clinical treatment paradigms are changing based on the expanding knowledge of complex pes planovalgus morphologies or progressive collapsing foot deformity, which is present in both neurologic and non-neurologic populations. Four patient cohorts were created from 10 flexible PCFD, 10 rigid PCFD, 10 adult cerebral palsy, and 10 asymptomatic control patients. Six coordinate systems were tested on both the talus and calcaneus for all groups. The aim of this study was to evaluate axes definitions for the subtalar joint across four different patient populations to determine the influence of morphology on the implementation of previously defined coordinate systems. Different morphologic presentations from various pathologies have a substantial impact on coordinate system definitions, given that numerous axes definitions are defined through geometric fits or manual landmark selection. Automated coordinate systems that align with clinically relevant anatomic planes are preferred. Principal component axes are automatic, but do not align with clinically relevant planes and should not be used for such analysis where anatomic planes are critical., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)