Abstract The aim of this study is to determine effects of size deviations of brachytherapy seeds on two dimensional dose distributions around the seed. Although many uncertainties are well known, the uncertainties which stem from geometric features of radiation sources are weakly considered and predicted. Neither TG-43 report which is not completely in common consensus, nor individual scientific MC and experimental studies include sufficient data for geometric uncertainties. Sizes of seed and its components can vary in a manufacturing deviation. This causes geometrical uncertainties, too. In this study, three seeds which have different geometrical properties were modeled using EGSnrc-Code Packages. Seeds were designed with all their details using the geometry package. 5% deviations of seed sizes were assumed. Modified seeds were derived from original seed by changing sizes by 5%. Normalizations of doses which were calculated from three kinds of brachytherapy seed and their derivations were found to be about 3%–20%. It was shown that manufacturing differences of brachytherapy seed cause considerable changes in dose distribution.