In this paper we present a new method for the determination of geometrical misalignments in cone-beam CT scanners, from the analysis of the projection data of a generic object. No a priori knowledge of the object shape and positioning is required. We show that a cost function, which depends on the misalignment parameters, can be defined using the projection data and that such a cost function has a local minimum in correspondence to the actual parameters of the system. Hence, the calibration of the scanner can be carried out by minimizing the cost function using standard optimization techniques. The method is developed for a particular class of 3D object functions, for which the redundancy of the fan beam sinogram in the transaxial midplane can be extended to cone-beam projection data, even at wide cone angles. The method has an approximated validity for objects which do not belong to that class; in that case, a suitable subset of the projection data can be selected in order to compute the cost function. We show by numerical simulations that our method is capable to determine with high accuracy the most critical misalignment parameters of the scanner, i.e., the transversal shift and the skew of the detector. Additionally, the detector slant can be determined. Other parameters such as the detector tilt, the longitudinal shift and the error in the source-detector distance cannot be determined with our method, as the proposed cost function has a very weak dependence on them. However, due to the negligible influence of these latter parameters in the reconstructed image quality, they can be kept fixed at estimated values in both calibration and reconstruction processes without compromising the final result. A trade-off between computational cost and calibration accuracy must be considered when choosing the data subset used for the computation of the cost function. Results on real data of a mouse femur as obtained with a small animal micro-CT are shown as well, proving the capability of the proposed calibration method. In principle, the method can be adapted to other cone-beam imaging modalities (e.g., single photon emission computed tomography).