PURPOSE: To determine the pattern of changes of rectum and bladder structures during conformal therapy of T3 prostate cancer and the impact of these changes on the accuracy of the dose-volume histograms (DVHs) and normal tissue complication probabilities (NTCPs) of these organs, based on the planning computed tomography (CT) scan only. METHODS AND MATERIALS: For 11 T3 prostate cancer patients treated with conformal therapy, three repeat CT scans were made in Weeks 2, 4, and 6 of the treatment. The bony anatomy was aligned with the planning CT scan, using three dimensional (3D) chamfer matching. The internal and external surfaces of rectum and bladder were contoured in each scan. Three volumes were calculated for each organ: solid organ (including filling), filling, and wall volume. DVHs and NTCPs were calculated for all structures. RESULTS: The solid organ and filling volumes varied considerably between patients and within a patient and they decreased with increasing treatment time. The largest patient variation was seen for patients with large initial filling volumes. The variations of rectum and bladder wall volumes during treatment were 9 and 17% (1 standard deviation (SD)), respectively, with no time trend. The changes of the high dose (> 80 and 90% of the prescribed dose) volumes of the rectum in response to rectum filling differences were proportional to the whole rectum volume changes. The variation of the high-dose rectum wall volume was relatively small (14%, 1 SD). As a result, the NTCPs of rectum and rectum wall were the same overall and the variation of the NTCPs during treatment was about 14% (1 SD) and not correlated with rectum filling. The variation of the high-dose bladder volumes (about 14%, 1 SD) was smaller than the variation of the whole bladder volumes (30%, 1 SD). The high-dose bladder wall volume decreased significantly due to wall distention as the bladder filling increased. As a result of this complex pattern, the variation of NTCPs of bladder (85%, 1 SD) and bladder wall (88%, 1 SD) during treatment was large and significantly correlated with bladder filling. CONCLUSIONS: The planning CT scan overestimates rectum and bladder filling during treatment. Furthermore, the variation of filling is so large that only the wall structures have relatively constant volumes during treatment. For the rectum wall, the DVHs and NTCPs, as estimated from the initial scan, are representative for the whole treatment, because no correlation was seen between these parameters and organ filling. For the bladder wall, however, such a correlation was present and consequently, the initial bladder wall DVHs and NTCPs can only be representative for the whole treatment, if the bladder filling can be kept reasonably constant during treatment.