Objectives: MRI is the preferred staging modality for rectal carcinoma patients. This work assesses the CT-MRI co-registration accuracy of four commercial rigid-body techniques for external beam radiotherapy treatment planning for patients treated in the prone position without fiducial markers. Methods: 17 patients with biopsy-proven rectal carcinoma were scanned with CT and MRI in the prone position without the use of fiducial markers. A reference co-registration was performed by consensus of a radiologist and two physicists. This was compared with two automated and two manual techniques on two separate treatment planning systems. Accuracy and reproducibility were analysed using a measure of target registration error (TRE) that was based on the average distance of the mis-registration between vertices of the clinically relevant gross tumour volume as delineated on the CT image. Results: An automated technique achieved the greatest accuracy, with a TRE of 2.3 mm. Both automated techniques demonstrated perfect reproducibility and were significantly faster than their manual counterparts. There was a significant difference in TRE between registrations performed on the two planning systems, but there were no significant differences between the manual and automated techniques. Conclusion: For patients with rectal cancer, MRI acquired in the prone treatment position without fiducial markers can be accurately registered with planning CT. An automated registration technique offered a fast and accurate solution with associated uncertainties within acceptable treatment planning limits. Randomised trials have demonstrated that adjuvant radiotherapy (RT) in patients with resectable rectal cancer offers a statistically significant reduction in the risk of local recurrence compared with surgery alone [1]. Two meta-analyses and a systematic review have confirmed this finding [2-4]: cancer-specific survival was found to be improved when RT was delivered with biological equivalent doses of .30 Gy pre-operatively. Two further trials have confirmed similar benefit when short-course pre-operative RT was combined with total mesorectal excision (TME) [5,6].Three further randomised trials have evaluated the role of pre-operative adjuvant chemoradiotherapy (CRT) for patients with stage T3-T4 or node-positive disease. Two of these studies demonstrated a reduction in local recurrence when pre-operative adjuvant CRT was used rather than long-course adjuvant RT alone [7,8]. The third study demonstrated both reduced local recurrence and reduced acute and late toxicity for pre-operative CRT compared with post-operative CRT [9]. The Cochrane review [4] also examined CRT and concluded that CRT provided incremental benefit in local control, irrespective of the timing of the chemotherapy. These results have led to a significant increase in the use of pre-operative radiation for patients with rectal cancer.MRI offers increased soft-tissue contrast compared with other radiographic imaging modalities such as CT. This improvement allows the accurate...