Purpose: Cone-beam CT (CBCT) projection images provide anatomical data in real-time over several respiratory cycles, forming a comprehensive picture of tumor movement. We developed and validated a method which uses these projections to determine the trajectory of and dose to highly mobile tumors during each fraction of treatment.Methods: CBCT images of a respiration phantom were acquired, the trajectory of which mimicked a lung tumor with high amplitude (up to 2.5 cm) and hysteresis. A template-matching algorithm was used to identify the location of a steel BB in each CBCT projection, and a Gaussian probability density function for the absolute BB position was calculated which best fit the observed trajectory of the BB in the imager geometry. Two modifications of the trajectory reconstruction were investigated: first, using respiratory phase information to refine the trajectory estimation (Phase), and second, using the Monte Carlo (MC) method to sample the estimated Gaussian tumor position distribution. The accuracies of the proposed methods were evaluated by comparing the known and calculated BB trajectories in phantom-simulated clinical scenarios using abdominal tumor volumes.Results: With all methods, the mean position of the BB was determined with accuracy better than 0.1 mm, and root-mean-square (RMS) trajectory errors averaged 3.8±1.1% of the marker amplitude. Dosimetric calculations using Phase methods were more accurate, with mean absolute error less than 0.5%, and with error less than 1% in the highest-noise trajectory. MC-based trajectories prevent the over-estimation of dose, but when viewed in an absolute sense, add a small amount of dosimetric error (<0.1%).Conclusions: Marker trajectory and target dose-of-the-day were accurately calculated using CBCT projections. This technique provides a method to evaluate highly-mobile tumors using ordinary CBCT data, and could facilitate better strategies to mitigate or compensate for motion during SBRT.This manuscript was submitted to Medical Physics