The use of a new integrated CT/LINAC combination, in which the CT scanner is inside the treatment room, and the same patient couch is used for CT scanning and treatment, should allow for accurate and precise correction of interfractional set-up errors. Comparison of intentional shifts in phantom position as detected by the CT system with shifts detected by an ultrasound localization device commonly used for prostate localization, and by an electronic portal imaging device, showed the standard deviation of set-up uncertainties to be within 1 mm in all directions for each modality. The agreement between the modalities was within 2.6 mm, 1.6 mm and 1.7 mm in the superior-inferior (SI), anterior-posterior (AP) and right-left (RL) directions, respectively. All these modalities are, therefore, suitable for image-guided radiation therapy applications. The choice of modality can be made based of factors such as anatomical site, inter-user variations, and patient set-up.