A new integrated CT/LINAC combination, in which the CT scanner is inside the radiation therapy treatment room and the same patient couch is used for CT scanning and treatment (after a 180-degree couch rotation), should allow for accurate correction of interfractional setup errors. The purpose of this study was to evaluate the sources of uncertainties, and to measure the overall precision of this system. The following sources of uncertainty were identified: (1) the patient couch position on the LINAC side after a rotation, (2) the patient couch position on the CT side after a rotation, (3) the patient couch position as indicated by its digital readout, (4) the difference in couch sag between the CT and LINAC positions, (5) the precision of the CT coordinates, (6) the identification of fiducial markers from CT images, (7) the alignment of contours with structures in the CT images, and (8) the alignment with setup lasers. The largest single uncertainties (one standard deviation or 1 SD) were found in couch position on the CT side after a rotation (0.5 mm in the RL direction) and the alignment of contours with the CT images (0.4 mm in the SI direction). All other sources of uncertainty are less than 0.3 mm (1 SD). The overall precision of two setup protocols was investigated in a controlled phantom study. A protocol that relies heavily on the mechanical integrity of the system, and assumes a fixed relationship between the LINAC isocenter and the CT images, gave a predicted precision (1 SD) of 0.6, 0.7, and 0.6 mm in the SI, RL and AP directions, respectively. The second protocol reduces reliance on the mechanical precision of the total system, particularly the patient couch, by using radio-opaque fiducial markers to transfer the isocenter information from the LINAC side to the CT images. This protocol gave a slightly improved predicted precision of 0.5, 0.4, and 0.4 mm in the SI, RL and AP directions, respectively. The distribution of phantom position after CT-based correction confirmed these results. Knowledge of the individual sources of uncertainty will allow alternative setup protocols to be evaluated in the future without the need for significant additional measurements.