Background: To study and analyze the variations in delivered doses to rectum and bladder of carcinoma prostate patients by using kilo Voltage (kV) ‘Cone Beam Computed Tomography’ (CBCT) images. Materials and Methods: 2-Dimensional kilo Voltage (2D kV) Imaging and CBCT were done for seven prostate cancer patients. The deviations among their shifts were correlated and the volumetric changes of the rectum and bladder were analyzed. Rectum and bladder contours were redrawn on every boost fractions and dose calculation were performed on CBCT images to study the effect on dose volume histograms. Results: A correlation coefficient for set-up variations was within 0.78 for all directions between CBCT soft tissue matching and kV bone match. The mean deviation of bladder and rectum volume over the boost fractions was -12% to +9% (SD 31cc to 70cc) and -10.2% to+12% (SD 3.1cc to14.9cc), respectively. Bladder mean dose variation was <1.5Gy for all three positions whereas it was <3.65Gy for rectum. D1% dose deviation from reference plan for bladder was 1.1Gy (CBCT matched position), 1.4Gy (kV matched position), and 1.7Gy (no correction), and for rectum, the deviations were 1.2Gy, 2.2Gy, 3.6Gy, respectively. No significant deviation was found statistically significant at the low dose region. Conclusion: It is possible to achieve good dose delivery and conformity in target (prostate) with CBCT image guidance rather than kV bone match, but dose contribution to the rectum is dependent on the patient’s anatomy, bladder filling, and rectum filling, pertaining to the day of examination.