This project develops atlas‐based deformable image registration methods to map electron densities and automatically segment organs on MRI scans. This will enable dose calculations to be performed using the MRI scan without the requirement for an additional CT scan. The method developed uses atlas‐based deformable image registration. An MRI atlas was developed based on whole pelvic MRI scans for 39 patients. The atlas is then registered to an individual patient MRI scan. The registration of the atlas organ contours gives the automatically segmented organs on that patient scan. A CT or electron‐density atlas was also developed that corresponds to the MRI atlas. The deformation vectors that register the MRI‐atlas to the patient MRI scan are applied to the CT‐atlas to produce a pseudo‐CT scan for the patient. This can then be used for dose planning and digitally reconstructed radiographs. The feasibility of the entire workflow has been tested for one patient. The rectum, bladder, prostate and bone were automatically segmented on the MRI scan with Dice coefficient results of 0.82, 0.59, 0.62 and 0.81. The patient's plan was applied to the pseudo‐CT using a commercial treatment planning system. Dose at the normalisation point was 2.9% lower than on the full density CT plan. This method will improve the workflow of prostate radiotherapy planning and will reduce systematic uncertainties introduced by MRI‐CT registration. © 2010, American Association of Physicists in Medicine. All rights reserved.