We have developed a high‐precision system for calculating patient positional displacement between digital radiography images (DRs) and digitally reconstructed radiography images (DRRs), to reduce the radiation exposure to patients, minimize individual differences among radiological technologists, and decrease the positioning time for carbon ion radiotherapy. In this study, to clarify the practicality of the system, the accuracy of this system was evaluated relative to our setup tolerance using clinical data from patients with tumors at five sites. Moreover, the dependence of calculation accuracy on the size of the region of interest (ROI) and initial positioning parameters were evaluated for each site. It may be useful to know the initial positional dependence to calculate the limits of our system.