We investigated the setup variations over the treatment courses of 113 patients with intact prostate treated with 78Gy/39fx. Institutional standard bladder and bowel preparation and image guidance protocols were used in CT simulation and treatment. The RapidArc treatment plans were optimized in Varian Eclipse treatment planning system and delivered on Varian 2100X Clinacs equipped with On-Board Imager to localize the target before beam-on. The setup variations were calculated in terms of mean and standard deviation of couch shifts. No correlation was observed between the mean shift and standard deviation over the treatment course and patient age, initial prostate volume and rectum size. The mean shifts in the first and last 5 fractions are highly correlated (P < 10−10) while the correlation of the standard deviations cannot be determined. The Mann-Kendall tests indicate trends of the mean daily Ant-Post and Sup-Inf shifts of the group. The target is inferior by ∼1mm to the planned position when the treatment starts and moves superiorly, approaching the planned position at 10th fraction, and then gradually moves back inferiorly by ∼1mm in the remain fractions. In the Ant-Post direction, the prostate gradually moves posteriorly during the treatment course from a mean shift of ∼2.5mm in the first fraction to ∼1mm in the last fraction. It may be related to a systematic rectum size change in the progress of treatment. The biased mean shifts in Ant-Post and Sup-Inf direction of most patients suggest systematically larger rectum and smaller bladder during the treatment than at CT simulation.