PURPOSE: Knowledge about the mobility of organs relative to the bony anatomy is of great importance when preparing and verifying conformal radiotherapy. The conventional technique for measuring the motion of an organ is to locate landmarks on the organ and the bony anatomy and to compare the distance between these landmarks on subsequent computerized tomography (CT) scans. The first purpose of this study is to investigate the use of a three dimensional (3D) image registration method based on chamfer matching for measurement of the location and orientation of the whole organ relative to the bony anatomy. The second purpose is to quantify organ motion during conformal therapy of the prostate. METHODS AND MATERIALS: Four CT scans were made during the course of conformal treatment of 11 patients with prostate cancer. With the use of a 3D treatment planning system, the prostate and seminal vesicles were contoured interactively. In addition, bladder and rectum were contoured and the volume computed. Next, the bony anatomy of subsequent scans was segmented and matched automatically on the first scan. The femora and the pelvic bone were matched separately to quantify motion of the legs. Prostate (and seminal vesicle) contours from the subsequent scans were matched on the corresponding contours of the first scan, resulting in the 3D rotations and translations that describe the motion of the prostate and seminal vesicles relative to the pelvic bone. RESULTS: Bone matching of two scans with about 50 slices of 256 x 256 pixels takes about 2 min on a workstation and achieves subpixel registration accuracy. Matching of the organ contours takes about 30 s. The accuracy in determining the relative movement of the prostate is 0.5 to 0.9 mm for translations (depending on the axis) and 1 degree for rotations (standard deviations). Because all organ contours are used for matching, small differences in delineation of the prostate, missing slices, or differences in slice distance have only a limited influence on the accuracy. Rotations of the femora and the pelvic bone are quantified with about 0.4 degree accuracy. A strong correlation was found between rectal volume and anterior-posterior translation and rotation around the left-right axis of the prostate. Consequently, these parameters had the largest standard deviations of 2.7 mm and 4.0 degrees. Bladder filling had much less influence. Less significant correlations were found between various leg rotations and pelvic and prostate motion. Standard deviations of the rotation angles of the pelvic bone were less than 1 degree in all directions. CONCLUSIONS: Using 3D image registration, the motion of organs relative to bony anatomy has been quantified accurately. Uncertainties in contouring and visual interpretation of the scans have a much smaller influence on the measurement of organ displacement with our new method than with conventional methods. We have quantified correlations between rectal filling, leg motions, and prostate motion.