The problem of microbial growth in fuels, especially biofuels, is a very important issue. Water is a necessity for microbial growth to occur. Unfortunately, it is very hard to exclude all water from fuel systems during daily operations, especially when biodiesel is added to the fuel mix. The aim of this work was to investigate the impact of ionizing radiation on selected properties of fatty acids methyl esters in order to evaluate the possibility of using irradiation techniques to sterilize biodiesel and its blends. Ionizing radiation influences the chemical composition of biodiesel samples containing especially unsaturated bonds. Irradiation was performed in a specially designed flow system. The tested parameters were compared with the normative values from the ISO 14214 standard. Density, kinematic viscosity, flash point, water content and cold filter plugging point as a macroscopic parameters do not change despite their irradiation with ionizing radiation. Change was observed in microscopic parameters as oxidation stability and esters content. During irradiation, Rapeseed Methyl Ester (RME) samples formed oxidation products, which lower the oxidative stability. It was observed that, for esters content, requirements of the standard could be met in the case of using very small doses. In the case of RME samples saturated with water, the changes in the ester concentration were smaller, but the resulting products decreased the oxidation stability. Sterilization fatty acids methyl esters (FAME) was observed with the use of e beam radiation is to apply very low doses (up to 2 kGy) in a flow system without adding water. Sterilization FAME saturated by water requires the use of higher doses of radiation, which adversely affects the oxidative stability.