The objectives of this study were to estimate global uncertainty for patients with thoracic tumors treated in our center using the CyberKnife VSI after placement of fiducial markers and to compare our findings with the standard CTV to PTV margins used to date. Datasets for 16 patients (54 fractions) treated with the CyberKnife and the Synchrony Respiratory Tracking System were analyzed retrospectively based on CT planning, tracking information, and movement data generated and saved in the logs files by the system. For each patient, we analyzed all the main uncertainty sources and assigned a value. We also calculated an expanded global uncertainty to ensure a robust estimation of global uncertainty and to enable us to determine the position of 95% of the CTV points with a 95% confidence level during treatment. Based on our estimation of global uncertainty and compared with our general margin criterion (5 mm in all three directions: superior/inferior [SI], anterior/posterior [AP], and lateral [LAT]), 100% were adequately covered in the LAT direction, as were 94% and 94% in the SI and AP directions. We retrospectively analyzed the main sources of uncertainty in the CyberKnife process patient by patient. This individualized approach enabled us to estimate margins for patients with thoracic tumors treated in our unit and compare the results with our standard 5 mm margin.PACS number: 87.55‐x