All authors contributed equally A specially constructed highly-mobile electron accelerator is being developed for Intra Operative Radiation Therapy (IORT) in Poland. The aim of this work was to study the effects of different materials and geometry of accelerator head components on such critical beam properties as flatness, X-ray and neutron contamination, and the amount of dose delivered outside the treatment field. Based on these findings, a treatment head and applicators for the new mobile electron accelerator are being designed. The Monte Carlo code, BEAMnrc/EGSnrc, was used to build two models of a treatment head with plastic and metal applicators. FLUKA code was used for beam-stopper and shielding estimations. Both models fulfill basic requirements for quality of the therapeutic beam, as well as for radiation protection against stray and leakage radiation. The new aspects of our study were simulations for applicators with diameters of 15 and 22 cm for larger field intra operative treatment, which are not generally available on the market.