In this study, we analyzed planning organ at risk volume (PRV) for the rectum using a series of cone beam computed tomographies (CBCTs) acquired during the treatment of prostate cancer and evaluated the dosimetric effect of different PRV definitions. Overall, 21 patients with prostate cancer were treated radically with 78Gy in 39 fractions had in total 418 CBCTs, each acquired at the end of the first 5 fractions and then every alternate fraction. The PRV was generated from the Boolean sum volume of the rectum obtained from first 5 fractions (PRV-CBCT-5) and from all CBCTs (PRV-CBCT-All). The PRV margin was compared at the superior, middle, and inferior slices of the contoured rectum to compare PRV-CBCT-5 and PRV-CBCT-All. We also compared the dose received by the planned rectum (Rectum-computed tomography [CT]), PRV-CBCT-5, PRV-CBCT-All, and average rectum (CBCT-AV-dose-volume histogram [DVH]) at critical dose levels. The average measured rectal volume for all 21 patients for Rectum-CT, PRV-CBCT-5, and PRV-CBCT-All was 44.3 ± 15.0, 92.8 ± 40.40, and 121.5 ± 36.7cm(3), respectively. For PRV-CBCT-All, the mean ± standard deviation displacement in the anterior, posterior, right, and left lateral directions in centimeters was 2.1 ± 1.1, 0.9 ± 0.5, 0.9 ± 0.8, and 1.1 ± 0.7 for the superior rectum; 0.8 ± 0.5, 1.1 ± 0.5, 1.0 ± 0.5, and 1.0 ± 0.5 for the middle rectum; and 0.3 ± 0.3; 0.9 ± 0.5; 0.4 ± 0.2, and 0.5 ± 0.3 for the inferior rectum, respectively. The first 5 CBCTs did not predict the PRV for individual patients. Our study shows that the PRV margin is different for superior, middle, and the inferior parts of the rectum, it is wider superiorly and narrower inferiorly. A uniform PRV margin does not represent the actual rectal variations during treatment for all treatment fractions. The large variation in interpatient rectal size implies a potential role for adaptive radiotherapy for prostate cancer.