Deformable image registration (DIR) is increasingly used in radiotherapy applications and provides the basis for a previously described model of patient-specific respiratory motion. We examine the accuracy of a DIR algorithm and motion model with respiration-correlated CT (RCCT) images of software phantom with known displacement fields; physical deformable abdominal phantom with implanted fiducials in liver; and small liver structures in patient images. The motion model is derived from a principal component analysis that relates volumetric deformations with the motion of the diaphragm or fiducials in the RCCT. Patient data analysis compares DIR with rigid registration as ground truth: the mean ± standard deviation in 3D discrepancy in liver structure centroid position is 2.0 ± 1.0 mm. DIR discrepancy in software phantom is 3.8 ± 2.0 mm in lung and 3.7 ± 1.8 mm in abdomen; discrepancies near chest wall are larger than indicated by image feature matching. Marker 3D discrepancy in physical phantom is 3.6 ± 2.8 mm. The results indicate that visible features in the images are important for guiding the DIR algorithm. Motion model accuracy is comparable to DIR, indicating that two principal components are sufficient to describe DIR-derived deformation in these data sets.