The purpose of this study is to determine the influence of bladder and bowel preparation protocols on the dose-volume histograms (DVHs) of these organs using the cone beam computed tomography (CBCT)-based intensity modulated radiotherapy (IMRT) treatment planning for prostate cancer patients. The pelvic DVHs of 12 prostate cancer patients were studied using CBCT images obtained immediately before each treatment. Six patients had bladder and bowel preparation protocol whilst the other six patients were the control group. Contoured bladder and rectal volumes on CBCT images were compared with planning computed tomography. All patients were treated with IMRT with 7800 cGy in 39 fractions over 8 weeks. Compared with the patient with bladder preparation protocol, patients without bladder preparation instruction had higher bladder volume and dose variation. The maximum variation in bladder volume was as high as 98% in the control group. Without bowel preparation protocol, the rectal volumes were more variability. Owing to changes in rectal filling on the day of treatment, the maximum variation in rectal volume was as high as + 96%. With bowel preparation protocol, the maximum rectum volume variations were less than 25%. The changes in prostate target dose compared with planning dose were minimal as would be expected from positioning with daily image guidance and gold seed implanted.