We present the results of a pilot study designed to investigate methods that may be applied to develop a patient position correction protocol for the post-prostatectomy patient receiving radiotherapy. Imaging was carried out with cone beam CT (CBCT) to investigate its suitability for detecting changes in rectal and bladder volumes and movements of these organs relative to the treatment planning CT. Eligible patients were imaged daily during the first week of treatment and weekly thereafter. Surrogate explanatory variables, including distance from the isocentre to the anterior rectum and bladder length, were tested for their potential to substitute for contouring entire organs and predict for changes in coverage of the planning treatment volume (PTV) by the 95% isodose (PTV95) and the maximum dose delivered to 50% of the rectal volume (RECTD50). The PTV defined on the CBCT images was larger than that defined on the planning CT and resulted in a decrease in the PTV95. Bladder length correlated with bladder volume and changes in bladder volume were associated with a decrease in PTV95. Rectal volumes changed randomly during treatment. There was a trend for the rectum to move anteriorly as treatment progressed. CBCT may be used to define the PTV, rectum and bladder though the reason for an apparent increase in PTV on CBCT requires further investigation. The bladder length and distance to the anterior rectal wall are potential surrogate explanatory variables. Further studies will be designed to test values of these surrogates that predict the need for a change in isocentre position.