The MammoSite breast high dose rate brachytherapy is used in treatment of early-stage breast cancer. The tumour bed volume is irradiated with high dose per fraction in a relatively small number of fractions. Uncertainties in the source positioning and MammoSite balloon deformation will alter the prescribed dose within the treated volume. They may also expose the normal tissues in balloon proximity to excessive dose. The purpose of this work is to explore the impact of these two uncertainties on the MammoSite dose distribution in the breast using dose volume histograms and Monte Carlo simulations. The Lyman-Kutcher and relative seriality models were employed to estimate the normal tissues complications associated with the MammoSite dose distributions. The tumour control probability was calculated using the Poisson model. This study gives low probabilities for developing heart and lung complications. The probability of complications of the skin and normal breast tissues depends on the location of the source inside the balloon and the volume receiving high dose. Incorrect source position and balloon deformation had significant effect on the prescribed dose within the treated volume. A 4 mm balloon deformation resulted in reduction of the tumour control probability by 24%. Monte Carlo calculations using EGSnrc showed that a deviation of the source by 1 mm caused approximately 7% dose reduction in the treated target volume at 1 cm from the balloon surface. In conclusion, accurate positioning of the (192)Ir source at the balloon centre and minimal balloon deformation are critical for proper dose delivery with the MammoSite brachytherapy applicator. On the basis of this study, we suggest that the MammoSite treatment protocols should allow for a balloon deformation of < or = 2 mm and a maximum source deviation of < or = 1 mm.