We present a new method for rigid registration of CT datasets in 3D Radon space based on sparse sampling of scanning projections. The inputs are the two 3D Radon transforms of the CT scans, one densely sampled and the other sparsely sampled (limited number of scan angles/ranges). The output is the rigid transformation that best matches them. The method first finds the best matching between each projection direction vector in the sparse transform and the corresponding direction vector in the dense transform. It then solves a system of linear equations derived from the direction vector pairs (parallel-beam projections) or finds a solution by non-linear optimization (fan-beam and cone-beam projections). Experimental studies show that our method for 3D parallel beam registration outperforms image space registration in terms of convergence range with significantly reduced X-ray dose compared to a full conventional CT scan.