Silicon oxide based, aluminum gated MOS structures fabricated on n-type silicon were subjected to a low energy electron beam irradiation in the scanning electron microscope. The induced interface states and the oxide charges were studied by the high frequency capacitance–voltage technique as a function of the electron beam energy, irradiation dose, annealing time, temperature and electric field. Strong initial increase and subsequent saturation of the donor-like interface state density with the irradiation dose was observed for all electron beam energies used. Besides, shallow positively charged traps were found to be formed in the silicon oxide after irradiation, while at the initial stage of irradiation the formation of a negative charge was established. The irradiation induced interface states and the positively charged shallow oxide traps demonstrated notable reduction at room temperature. Zero bias annealing at the temperatures of about 250–300 °C resulted in a complete removal of the interface states and partial compensation or elimination of the oxidation induced positive fixed charge, presumably due to remaining negative charge in oxide.