Objectives To propose an automatic and accurate CARTO electroanatomic map (ECM) and CT surface registration algorithm for atrial fibrillation (AF) operations. Methods For each of the all 48 kinds of correspondence between the axes of the two images, the average distance of EAM to CT surface is estimated, and the one with the minimum distance is chosen as the registration result. Results Compared with Carto-Merge, the most often used software in AF operations, and the traditional stochastic approaches, principal axes based registration is automatic, fast, and accurate. Conclusions The proposed principal axes based method is valid for AF operations.