The present invention refers to 3D rotational X-ray imaging systems for use in computed tomography (CT) and, more particularly, to a fast, accurate and mathematically robust calibration method for determining the effective center of rotation (I) in not perfectly isocentric 3D rotational C-arm systems and eliminating substantially circular ring artifacts (RA) which arise when using such a CT scanner system for acquiring a set of 2D projection images of an object of interest to be three-dimensionally reconstructed. For this purpose, a C-arm based rotational CT scanner comprising at least one radiation detector (D) having an X-radiation sensitive surface exposed to an X-ray beam emitted by at least one X-ray tube (S), each rotating along a non-ideal circular trajectory (TF, TCD) about an object of interest to be three-dimensionally reconstructed from a set of 2D projection images is used for providing geometrical calibration data by scanning a calibration phantom from a plurality of distinct projection directions and calculating, for each projection direction, the 3D positions of the X-ray tube's focal spot and the X-ray detector's center. For approximating the exact 3D position and angular direction of the axis of rotation about which the at least one X-ray tube and the at least one radiation detector rotate, a circular regression technique using a number of mathematically robust least squares fits is applied.