The goal of this project is to investigate quantitatively the performance of different deformable image registration algorithms (DIR) with helical (HCT), axial (ACT), and cone‐beam CT (CBCT). The variations in the CT‐number values and lengths of well‐known targets moving with controlled motion were evaluated. Four DIR algorithms: Demons, Fast‐Demons, Horn‐Schunck and Lucas‐Kanade were used to register intramodality CT images of a mobile phantom scanned with different imaging techniques. The phantom had three water‐equivalent targets inserted in a low‐density foam with different lengths (10–40 mm) and moved with adjustable motion amplitudes (0–20 mm) and frequencies (0–0.5 Hz). The variations in the CT‐number level, volumes and shapes of these targets were measured from the spread‐out of the CT‐number distributions. In CBCT, most of the DIR algorithms were able to produce the actual lengths of the mobile targets; however, the CT‐number values obtained from the DIR algorithms deviated from the actual CT‐number of the targets. In HCT, the DIR algorithms were successful in deforming the images of the mobile targets to the images of the stationary targets producing the CT‐number values and lengths of the targets for motion amplitudes <20 mm. Similarly in ACT, all DIR algorithms produced the actual CT‐number values and lengths of the stationary targets for low‐motion amplitudes <15 mm. The optical flow‐based DIR algorithms such as the Horn‐Schunck and Lucas‐Kanade performed better than the Demons and Fast‐Demons that are based on attraction forces particularly at large motion amplitudes. In conclusion, most of the DIR algorithms did not reproduce well the CT‐number values and lengths of the targets in images that have artifacts induced by large motion amplitudes. The deviations in the CT‐number values and variations in the volume of the mobile targets in the deformed CT images produced by the different DIR algorithms need to be considered carefully in the treatment planning for accurate dose calculation dose coverage of the tumor, and sparing of critical structures.