Little is known about the three-dimensional behavior of the anterior cruciate ligament (ACL) reconstructed knee during dynamic, functional loading, or how dynamic knee function changes over time in the reconstructed knee. We hypothesized dynamic, in vivo function of the ACL-reconstructed knee is different from the contralateral, uninjured knee and changes over time. We measured knee kinematics for 16 subjects during downhill running 5 and 12 months after ACL reconstruction (bone-patellar tendon-bone or quadrupled hamstring tendon with interference screw fixation) using a 250 frame per second stereoradiographic system. We used repeated-measures ANOVA to ascertain whether there were differences between the uninjured and reconstructed limbs and over time. We found no differences in anterior tibial translation between limbs, but reconstructed knees were more externally rotated and in more adduction (varus) during the stance phase of running. Anterior tibial translation increased from 5 to 12 months after surgery in the reconstructed knees. Anterior cruciate ligament reconstruction failed to restore normal rotational knee kinematics during dynamic, functional loading and some degradation of graft function occurred over time. These abnormal motions may contribute to long-term joint degeneration associated with ACL injury and reconstruction.