Damage to the anterior cruciate and medial collateral ligaments is a common injury in the human knee joint, causing pain and joint instability, and leading to an increased incidence of osteoarthritis. The ovine stifle joint provides an animal model in which to simultaneously investigate joint mechanics and joint biology in vivo. The foundation of this work was the development and validation of an accurate method for the measurement of dynamic in vivo kinematics of the ovine stifle joint. This method was shown to have sufficient accuracy and repeatability to detect small changes in position at the joint surface (0.4±0.4 mm) and to be used for serial measurements over time. Joint kinematics were measured in the intact ovine stifle joint, providing subject specific baseline data. Kinematics were then measured serially after either combined transection of the anterior cruciate and medial collateral ligaments, or sham surgery without transection. Within subject changes in kinematics were investigated at 2, 4, 8, 12, 16, and 20 weeks after the intervention. Changes in the transected group were compared with changes in the sham group to determine the impact of ligament transection on joint kinematics. At 2 and 20 weeks after surgical intervention, the maximal anterior tibial position was significantly increased during mid-stance in the transected group (4.9±0.9 mm and 5.8±1.9 mm) compared to the sham operated group (0.2±0.2 mm and -0.1±0.1 mm). Early changes in joint flexion angle had normalized by 20 weeks after transection, but in addition to the anterior shift, the joint was significantly adducted (0.5±0.7°), and shifted in the medial (2.5±1.2 mm) and superior directions (1.6±0.4 mm). These changes in joint position after transection were shown to impact the joint system as a whole, with changes in the mechanical environment of the ligaments, the relative position and separation of the subchondral surfaces, and the magnitudes and directions of the relative velocities between the tibia and femur at the subchondral surfaces. These changes in the mechanical environment of the joint are expected to play a role in the degeneration of articular cartilage that is observed in this model of osteoarthritis.