This paper discusses a novel strategy for estimating projection matrices using the contours of anatomical structures tracked on x-ray projection images. It establishes an auto-calibration routine which calculates the geometrical projection parameters from unknown patient geometry based on iterative reconstruction and registration. By introducing the uncertainty of calibration parameters in registration, we achieve a robust correction for broad types of patient motion. As our method does not rely on consistency between projection data and tomography reconstruction it is robust towards truncation, noise and other typical artifacts of CBCT reconstruction. We evaluated our proposed method of auto-calibration on digital reconstructed radiographs (DRRs) of a CT headscan. In a standard dental CBCT setup our approach shows an average recovery of volume sharpness of 83:67% for different motion types.