In many cases, radio-frequency catheter ablation of the pulmonary veins attached to the left atrium still involves fluoroscopic image guidance. Two-dimensional X-ray navigation may also take advantage of overlay images derived from static pre-operative 3D volumetric data to add anatomical details otherwise not visible under X-ray. Unfortunately, respiratory motion may impair the utility of static overlay images for catheter navigation. We developed a novel approach for image-based 3D motion estimation and compensation as a solution to this problem. It is based on 3D catheter tracking which, in turn, relies on 2D/3D registration. To this end, a bi-plane C-arm system is used to take X-ray images of a special circumferential mapping catheter from two directions. In the first step of the method, a 3D model of the device is reconstructed. Three-dimensional respiratory motion at the site of ablation is then estimated by tracking the reconstructed catheter model in 3D based on bi-plane fluoroscopy. Phantom data and clinical data were used to assess model-based catheter tracking. Our phantom experiments yielded an average 2D tracking error of 1.4mm and an average 3D tracking error of 1.1mm. Our evaluation of clinical data sets comprised 469 bi-plane fluoroscopy frames (938 monoplane fluoroscopy frames). We observed an average 2D tracking error of 1.0 + or - 0.4mm and an average 3D tracking error of 0.8 + or - 0.5mm. These results demonstrate that model-based motion-compensation based on 2D/3D registration is both feasible and accurate.