Abstract: This invention describes a system and method for aligning radiation therapy beams with a treatment target of a patient. Diagnostic computer tomography scanning is used to map the treatment target in the patient's anatomy and to aid physicians in deciding where to aim the radiation therapy beams. Digitally reconstructed radiographs are generated from an intermediate 3-D image produced from the CT scans. These DRRs are compared with x-ray images taken of the treatment target's position taken at the time of treatment. A transformation equation is used to compare the DRRs and the x-ray images. A minimization equation is used to determine the similarity between the two sets of images. If the difference between the two sets fall below a determined minimum value, then the position of the treatment target is deemed correct and the radiation therapy begins.