Kinematics of the foot during static and dynamic tasks are technically challenging to accurately measure, making it difficult to evaluate their contribution to running-related injuries. Motion capture can detect changes in running mechanics, such as with differing footwear. Habitual barefoot runners and/habitual minimalist shoe runners underwent a biomechanical evaluation of their foot movement during running using reflective markers and optical motion capture. A five-segment foot model was used to compare motions between the different parts of the foot while running barefoot and wearing Vibram Five Fingers™ (VFF) barefoot mimicking shoes. Supination/pronation in the forefoot was larger but not significant between habitual shod and habitual VFF runners. In contrast, the other foot motions (forefoot spreading/rising, hindfoot pronation/supination and hindfoot adduction/abduction) were not significantly different between the groups of runners. Therefore it could be possible that transitioning from a regular running shoe to a barefoot mimicking minimalist shoe would cause the foot to adopt a more supinated gait cycle.