This paper describes a methodology for the analysis of three-dimensional (3-D) kinematics of live joints of the foot based on tomographic image data acquired via magnetic resonance (MR) imaging. A mechanical jig facilitates acquisition of MR images corresponding to different positions of the joint in a pronation-supination motion. The surfaces of the individual tarsal bones are constructed by segmenting the MR images. A mathematical description of the motion of the individual bones and of their relative motion is derived by computing the rigid transformation required to match the centroids and the principal axes of the surfaces. The mathematically described motion is animated via surface renditions of the bones. The kinematics of the bones are analyzed based on features extracted from the motion description and on how they vary with motion. Based on 17 joints that have been imaged, which includes an abnormal joint and the same joint after surgical correction, we conclude that this methodology offers a practical tool for measuring internal 3-D kinematics of joints in vivo and for characterizing and quantifying with specificity normal kinematics and their pathological deviations. Some of the 3-D kinematic animations generated using the methods of this paper for normal joints can be seen at: http:(/)/www.mipg.upenn.edu.