Segment coordinate systems (CSs) of marker-based multi-segment foot models are used to measure foot kinematics, however their relationship to the underlying bony anatomy is barely studied. The aim of this study was to compare marker-based CSs (MCSs) with bone morphology-based CSs (BCSs) for the hindfoot and forefoot. Markers were placed on the right foot of fifteen healthy adults according to the Oxford, Rizzoli and Amsterdam Foot Model (OFM, RFM and AFM, respectively). A CT scan was made while the foot was loaded in a simulated weight-bearing device. BCSs were based on axes of inertia. The orientation difference between BCSs and MCSs was quantified in helical and 3D Euler angles. To determine whether the marker models were able to capture inter-subject variability in bone poses, linear regressions were performed. Compared to the hindfoot BCS, all MCSs were more toward plantar flexion and internal rotation, and RFM was also oriented toward more inversion. Compared to the forefoot BCS, OFM and RFM were oriented more toward dorsal and plantar flexion, respectively, and internal rotation, while AFM was not statistically different in the sagittal and transverse plane. In the frontal plane, OFM was more toward eversion and RFM and AFM more toward inversion compared to BCS. Inter-subject bone pose variability was captured with RFM and AFM in most planes of the hindfoot and forefoot, while this variability was not captured by OFM. When interpreting multi-segment foot model data it is important to realize that MCSs and BCSs do not always align.