Over the last decade, increased effort has been made to acquire three dimensional images of knee joints under weight-bearing condition. Cone-beam CT systems are popular because of their high flexibility with respect to patient position and scan trajectory. However, scans in a standing or squatting patient position are affected by involuntary patient motion during the acquisition, which results in streaking and blurring artifacts in the reconstructed volumes. Previous work suggested the use of fiducial markers to estimate and compensate for motion artifacts. However, marker placement on the skin might not accurately reflect the motion at the center of the joint. In this work, we propose a marker-free motion compensation method that is based on 2D/3D rigid registrations of individual projection images to a segmentation of the bones from a prior, motion-free scan. The estimated motion of the individual bones is then combined to a global motion field to allow for a motion compensated reconstruction. Qualitative and quantitative results show substantial improvement compared to uncorrected images. Incorporating smoothness constraints into the estimated motion parameters during the registration further improved the results.