We report the setup reproducibility of thoracic and upper gastrointestinal (UGI) radiotherapy (RT) patients for 2 immobilization methods evaluated through cone-beam computed tomography (CBCT) image guidance, and present planning target volume (PTV) margin calculations made on the basis of these observations. Daily CBCT images from 65 patients immobilized in a chestboard (CB) or evacuated cushion (EC) were registered to the planning CT using automatic bony anatomy registration. The standardized region-of-interest for matching was focused around vertebral bodies adjacent to tumor location. Discrepancies >3 mm between the CBCT and CT datasets were corrected before initiation of RT and verified with a second CBCT to assess residual error (usually taken after 90 s of the initial CBCT). Positional data were analyzed to evaluate the magnitude and frequencies of setup errors before and after correction. The setup distributions were slightly different for the CB (797 scans) and EC (757 scans) methods, and the probability of adjustment at a 3-mm action threshold was not significantly different ( p = 0.47). Setup displacements >10 mm in any direction were observed in 10% of CB fractions and 16% of EC fractions ( p = 0.0008). Residual error distributions after CBCT guidance were equivalent regardless of immobilization method. Using a published formula, the PTV margins for the CB were L/R, 3.3 mm; S/I, 3.5 mm; and A/P, 4.6 mm), and for EC they were L/R, 3.7 mm; S/I, 3.3 mm; and A/P, 4.6 mm. In the absence of image guidance, the CB slightly outperformed the EC in precision. CBCT allows reduction to a single immobilization system that can be chosen for efficiency, logistics, and cost. Image guidance allows for increased geometric precision and accuracy and supports a corresponding reduction in PTV margin.