To compare the dosimetrical differences between plans generated by helical tomotherapy using 2D or 3D margining technique in in prostate cancer. Ten prostate cancer patients were included in this study. For 2D plans, planning target volume (PTV) was created by adding 5 mm (lateral/anterior-posterior) to clinical target volume (CTV). For 3D plans, 5 mm margin was added not only in lateral/anterior-posterior, but also in superior-inferior to CTV. Various dosimetrical indices, including the prescription isodose to target volume (PITV) ratio, conformity index (CI), homogeneity index (HI), target coverage index (TCI), modified dose homogeneity index (MHI), conformation number (CN), critical organ scoring index (COSI), and quality factor (QF) were determined to compare the different treatment plans. Differences between 2D and 3D PTV indices were not significant except for CI (p = 0.023). 3D margin plans (11195 MUs) resulted in higher (13.0%) monitor units than 2D margin plans (9728 MUs). There were no significant differences in any OARs between the 2D and 3D plans. Overall, the average 2D plan dose was slightly lower than the 3D plan dose. Compared to the 2D plan, the 3D plan increased average treatment time by 1.5 minutes; however, this difference was not statistically significant (p = 0.082). We confirmed that 2D and 3D margin plans are not significantly different with regard to various dosimetric indices such as PITV, CI, and HI for PTV, and OARs with tomotherapy.