The registration of multi-modal medical image data is important in the fields of image guided surgery and computer aided medical diagnosis. Registration accuracy is of utmost importance in both fields, however in the former, the speed of registration is equally important. In this paper, we present a point-based ‘fast’ non-rigid registration algorithm which exhibits significant speedups as compared to the non-optimised equivalent algorithm. Additionally, we make use of the parallel nature of the graphics processing unit (GPU) of the video adapter card of a standard PC to gain further speedups. The algorithm achieved sub-second performance when tested on the registration of MR with CT image data of size 2563.