It is essential for accurate image reconstruction to obtain a set of parameters that describes the x-ray scanning geometry. A geometric estimation method is presented for x-ray digital intraoral tomosynthesis (DIT) in which the detector remains stationary while the x-ray source rotates. The main idea is to estimate the three-dimensional (3-D) coordinates of each shot position using at least two small opaque balls adhering to the detector surface as the positioning markers. From the radiographs containing these balls, the position of each x-ray focal spot can be calculated independently relative to the detector center no matter what kind of scanning trajectory is used. A 3-D phantom which roughly simulates DIT was designed to evaluate the performance of this method both quantitatively and qualitatively in the sense of mean square error and structural similarity. Results are also presented for real data acquired with a DIT experimental system. These results prove the validity of this geometric estimation method.