The aim of this study was to evaluate the differences in target localization between Calypso®, kV orthogonal imaging and cone‐beam computed tomography (CBCT) for combined translations and rotations of an anthropomorphic pelvic phantom. The phantom was localized using all three systems in 50 different positions, with applied translational and rotational offsets randomly sampled from representative normal distributions of prostate motion. Lin's concordance correlation coefficient (ρc) and 95% confidence intervals were calculated to assess the agreement between the localization systems. Mean differences and difference vectors between the three systems were also calculated. Agreement between systems for lateral, vertical, and longitudinal translations was excellent, with ρc values of greater than 0.98 between all three systems in all axes. There was excellent agreement between the systems for rotations around the lateral axis (pitch) (ρc > 0.99), and around the vertical axis (yaw) (ρc > 0.97). However, somewhat poorer agreement for rotations around the longitudinal axis (roll) was observed, with the lowest correlation observed between Calypso and kV orthogonal imaging (ρc = 0.895). Mean differences between the phantom position reported by Calypso and the radiographic systems were less than 1 mm and 1° for all translations and rotations. The results for translations are consistent with the publications of previous authors. There is no comparable published data for rotations. While there is lower correlation between the three systems for roll than for the other angles, the mean differences in reported rotations are not clinically significant.