The aim of this study was to measure the setup variation for X (lateral), Y (longitude), and Z (vertical) by taking magnetic megavoltage computed tomography (MVCT) before treating the brain, oropharynx, lung, and prostate patients on helical tomotherapy. In this study, 30 patients were chosen for each of the treatment areas, and their skin was labeled with a mark on a treatment planning reference point when taking CT. We preceded MVCT prior to tomotherapy and then conducted an auto registration based on the bony landmarks; image registration was used for automatically matching the patient's setup. Lastly, we confirmed and evaluated the translation coordinates of the images for 30 patients. The following shows the comparison result of the setup errors of each part: X (lateral) showed the highest setup errors with <TEX>$3.44{\pm}2.05$</TEX> from Lung; Y (longitude) showed the highest setup errors showing <TEX>$3.40{\pm}2.87mm$</TEX> from Prostate; and Z (vertical) showed the highest setup errors showing <TEX>$6.62{\pm}4.38mm$</TEX> from Lung. This result verifies that the setup error can be prevented by taking MVCT before the treatment, and Planning Target Volume (PTV) margins can be reduced by referring to the resulting value of each treatment part. Ultimately, the dosage of the normal organs can be decreased as well as any side effects.