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Stereotactic body radiotherapy (SBRT) for lung and liver tumors is always performed under image guidance, a technique used to confirm the accuracy of setup positioning by fusing planning digitally reconstructed radiographs with X-ray, fluoroscopic, or computed tomography (CT) images, using bony structures, tumor shadows, or metallic markers as landmarks. The Japanese SBRT guidelines state that bony spinal structures should be used as the main landmarks for patient setup. In this study, we used the Novalis system as a linear accelerator for SBRT of lung and liver tumors. The current study compared the differences between spine registration and target registration and calculated total spatial accuracy including setup uncertainty derived from our image registration results and the geometric uncertainty of the Novalis system. We were able to evaluate clearly whether overall spatial accuracy is achieved within a setup margin (SM) for planning target volume (PTV) in treatment planning. After being granted approval by the Hospital and University Ethics Committee, we retrospectively analyzed eleven patients with lung tumor and seven patients with liver tumor. The results showed the total spatial accuracy to be within a tolerable range for SM of treatment planning. We therefore regard our method to be suitable for image fusion involving 2-dimensional X-ray images during the treatment planning stage of SBRT for lung and liver tumors.