A method of filling flexible foil bags, wherein a foil bag is shaped at least partially by a gaseous medium and is then filled with a liquid filling material, with the gaseous medium disinfecting the foil bag. Also, an apparatus for filling foil bags comprising a shaping unit for shaping the foil bags using a gaseous medium, a filling unit for filling the foil bags with a liquid medium, with the ability of adding a disinfecting effect to the gaseous medium.