An unbiased understanding of foot kinematics has been difficult to achieve due to the complexity of foot structure and motion. We have developed a protocol for evaluation of foot kinematics during barefoot walking based on a multi-segment foot model. Stereophotogrammetry was used to measure retroreflective markers on three segments of the foot plus the tibia. Repeatability was evaluated between-trial, between-day and between-tester using two subjects and two testers. Subtle patterns and ranges of motion between segments of the foot were consistently detected. We found that repeatability between different days or different testers is primarily subject to variability of marker placement more than inter-tester variability or skin movement. Differences between inter-segment angle curves primarily represent a shift in the absolute value of joint angles from one set of trials to another. In the hallux, variability was greater than desired due to vibration of the marker array used. The method permits objective foot measurement in gait analysis using skin-mounted markers. Quantitative and objective characterisation of the kinematics of the foot during activity is an important area of clinical and research evaluation. With this work we hope to have provided a firm basis for a common protocol for in vivo foot study.