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Background and Purpose This paper presents efficient and generalized processes for the clinical application of on-line X-ray volumetric cone-beam CT imaging (XVI) to improve the accuracy of patient set-up in radiation therapy. XVI image-guided therapy is illustrated by application to two contrasting sites, intra-cranial radiosurgery and prostate radiation therapy, with very different characteristics regarding organ motion, treatment precision, and imaging conditions. Patients and methods On-line set-up errors are determined in a two-step process. First the XVI data is registered to the planning data by matching the machine-isocenter with the planning-isocenter, respectively. The machine isocenter is defined in the XVI data during the reconstruction. The planning-isocenter is defined during the planning process in the planning CT data. Set-up errors are then determined from a second registration to remove residual displacements. The accuracy of the entire procedure for on-line set-up error correction was investigated in precision radiosurgery phantom studies. Results The phantom studies showed that sub-pixel size set-up errors (down to 0.5mm) can be correctly determined and implemented in the radiosurgery environment. XVI is demonstrated to provide quality skull detail enabling precise skull based on-line alignment in radiosurgery. A ‘local XVI' technique was found to give encouraging soft-tissue detail in the high-scatter pelvic environment, enabling on-line soft-tissue based set-up for prostate treatment. The two-step process for determination of set-up errors was found to be efficient and effective when implemented with a dedicated six panel interface enabling simultaneous visualization on the XVI and planning CT data sets. Conclusions XVI has potential to significantly improve the accuracy of radiation treatments. Present image quality is highly encouraging and can enable bony and soft-tissue patient set-up error determination and correction. As with all image guided treatment techniques the development of efficient procedures to utilize on-line data are of paramount importance.