A previously described system for modeling organ deformation using finite element analysis has been extended to permit dose calculation. Using this tool, the calculated dose to the liver during radiotherapy can be compared using a traditional static model (STATIC), a model including rigid body motion (RB), and finally a model that incorporates rigid body motion and deformation (RBD). A model of the liver, consisting of approximately 6000 tetrahedral finite elements distributed throughout the contoured volume, is created from the CT data obtained at exhale. A deformation map is then created to relate the liver in the exhale CT data to the liver in the inhale CT data. Six intermediate phase positions of each element are then calculated from their trajectories. The coordinates of the centroid of each element at each phase are used to determine the dose received. These intermediate dose values are then time weighted according to a population-modeled breathing pattern to determine the total dose to each element during treatment. This method has been tested on four patient datasets. The change in prescribed dose for each patient's actual tumor as well as a simulated tumor of the same size, located in the superior, intermediate, and inferior regions of the liver, was determined using a normal tissue complication model, maintaining a predicted probability of complications of 15%. The average change in prescribed dose from RBD to STATIC for simulated tumors in the superior, intermediate, and inferior regions are 4.0 (range 2.1 to 5.3), -3.6 (range -5.0 to -2.2), and -14.5 (range -27.0 to -10.0) Gy, respectively. The average change in prescribed dose for the patient's actual tumor was -0.4 Gy (range -4.1 to 1.7 Gy). The average change in prescribed dose from RBD to RB for simulated tumors in the superior, intermediate, and inferior regions are -0.04 (range -2.4 to 2.2), 0.2 (range -1.5 to 1.9), and 3.9 (range 0.8 to 7.3) Gy, respectively. The average change in the prescribed dose for the patient's actual tumor was 0.7 Gy (range 0.2 to 1.1 Gy). This patient sampling indicates the potential importance of including deformation in dose calculations.