A fill assembly sterilization method and system for a blow/fill/seal machine utilizes a closed loop circulation of sterilant containing gas. A typical sterilant is nitrogen dioxide in humidified air. The closed loop includes a shroud that defines a plenum and encloses the fill system. Optionally, at least one high efficiency particulate absorption (HEPA) filter is provided in the closed loop. Sterility assurance level of 10−6 can be achieved by subjecting the fill system to the sterilizing gas for at least 20 minutes at a temperature in the range of about 18° C. to about 30° C. Preferred sterilant gas is humidified air containing about 10 to about 20 milligrams of nitrogen dioxide per liter.