To compare the image quality of cone beam CT (CBCT) with that of planning CT (pCT) scan, and quantify inter-observer differences in therapeutic indices based on these scans prior to the introduction of an adaptive radiation therapy protocol for bladder cancer. Four consecutive patients were selected with muscle invasive bladder cancer receiving radical dose radiation therapy. Four radiation oncologists specializing in genitourinary malignancies contoured the clinical target volume (CTV) and rectum on both a pCT and a randomly chosen CBCT of the same patient. A conformity index (CI) for CTV and the rectum was determined for both pCT and CBCT. The maximal lateral, anterior, posterior, cranial and caudal extensions of the CTV for both CT and CBCT were determined for each observer. Variation in volumes of both the CTV and rectum for both pCT and were also compared using Varian Eclipse planning software (Varian Medical Systems, Palo Alto, CA, USA). Using pCT the mean CI for the CTV was 0.79; using CBCT the mean CI for the CTV was 0.75. For the rectum, the mean CI for using CT was 0.80 and for CBCT was 0.74. Greatest variation on CBCT CTV contours was seen in the supero-inferior direction with variation up to 2.1 cm between different radiation oncologists. With the variation in CI for pCT and CBCT of the CTV and rectum (0.04 and 0.06 respectively), CBCT is not significantly inferior to the pCT in terms of inter-observer contouring variability.