In biomechanics of the knee joints, the definition of the cruciate ligament adhesion areas is discussed for the cruciate ligament reconstruction. Effective information can be expected to be fed back to the cruciate ligament reconstruction if accurate movement of the natural knee joints can be analyzed. Therefore, this study performed in vivo six-degree-of-freedom (6-DOF) motion analysis for natural knee joints with high precision using an image matching technique. The image matching technique was performed determining the strength of correlation between the X-ray images from a flat panel detector (FPD) and the computational simulated image from three-dimensional gray-scale model reconstructed using computed tomography (CT). Average root mean square errors of this technique were 0.84 mm for the in-plane translation, 0.17 mm for the out-of-plane translation, and 0.29 degrees for the rotation. We report the analysis of motion and displacement of cruciate ligament adhesion areas for the natural knee joint during walking activity. The roll-back motion and a motion for the screw home movement could be confirmed from the change in the length of the cruciate ligaments.