Purpose: To evaluate the IGRT repositioning shifts determined by MV Cone Beam CT and by CT on rails using an anthropomorphic phantom. Method and Materials: Two IGRT systems installed in the same Linac room were studied. The CT based IGRT has been used in our Siemens Primus since 2004. Recently, a MV conebeam CT (Siemens MVision) was implemented with the objective to reduce the therapist time to obtain the IGRT shifts. The shifts and the corresponding total time were evaluated using an anthropomorphic PIXY® phantom. CTs of the phantom were obtained for head‐and‐neck, pelvis and lung and treatment planning was generated in XIO‐CMS for each site. The set of images, structures and plans was sent to both IGRT stations. Bbs were placed on the phantom surface at the isocenter axis, as a reference for the daily CT images. For each plan the MVCBCT was obtained three times to determine its reproducibility for 5 and 8 MU protocols. The registration for MVCBCT was done automatically and verified with manual registration. The table was then flipped to the CT position and the images acquired. In this case the registration is done manually and the isocenter shift is obtained through the bbs position. The procedures ware repeated for all sites. The total time to obtain the shifts and the image quality were also registered. Results and Discussion: The reproducibility of the MVCBCT for different protocols was within 2 mm. The maximum difference for MVCBCT and CT was 4 mm. The MVCBCT has poor image for soft tissue, and the fusion registration is based on mutual information. The total time to obtain the shifts is about 3 min for the new system and 7 to 8 min for the CT based system. This study excludes any deviation due to patient rotation and internal changes.