The purpose of this study was to determine the changes in the axis of rotation of the knee that occur during the stance phase of running. Using intracortical pins, the three-dimensional skeletal kinematics of three subjects were measured during the stance phase of five running trials. The stance phase was divided into equal motion increments for which the position and orientation of the finite helical axes (FHA) were calculated relative to a tibial reference frame. Results were consistent within and between subjects. At the beginning of stance, the FHA was located at the midepicondylar point and during the flexion phase moved 20mm posteriorly and 10mm distally. At the time of peak flexion, the FHA shifted rapidly by about 10–20mm in proximal and posterior direction. The angle between the FHA and the tibial transverse plane increased gradually during flexion, to about 15° of medial inclination, and then returned to zero at the start of the extension phase. These changes in position and orientation of FHA in the knee should be considered in analyses of muscle function during human movement, which require moment arms to be defined relative to a functional rotation axis. The finding that substantial changes in axis of rotation occurred independent of flexion angle suggests that musculoskeletal models must have more than one kinematic degree-of-freedom at the knee. The same applies to the design of knee prostheses, if the goal is to restore normal muscle function