To compare finite-size pencil beam/equivalent path-length (FSPB/EPL) and Monte Carlo (MC) SBRT dose computations for serial tomotherapy and to quantitatively assess dose differences between the dose calculation methods. Based on 72 SBRT plans for pulmonary targets, FSPB/EPL, considering the inhomogeneous lung environment, and MC calculations were performed to establish differences between FSPB/EPL predicted dose and MC derived doses. Compared with MC, FSPB/EPL consistently overestimated minimum doses to the clinical target volume and planning target volumes by an average of 18.1+/-7.15% (range 4 to 33.4%), and 21.9+/-10.4% (range 1.2 to 45.5%), respectively. The respective mean target dose differences were 15.5+/-7.4% (2.8-36.4%) and 19.2+/-7.6% (3.6-40.1%). Deviations from MC doses were lesion size and location dependent, with smaller lesions completely embedded into lung parenchyma being most susceptible. Larger lesion in contact with mediastinum and chest wall showed lesser differences. In comparison with MC dose calculation, FSPB/EPL overestimates doses delivered to pulmonary SBRT targets. The observed dose differences may have impact on local tumor control rates, and may deserve consideration when using fast, but less accurate dose calculation methods.