A sterilization container system for sterilizing surgical instruments, having a lid secured to a base by latches. The latches are automatically disengaged when the latches' release arms are raised to form handles by which the lid can be easily and securely manipulated; while the latches are automatically engaged when the latches' release arms are lowered, sealing the lid to the base. The base is provided with an outer safety wall, which is lower than and which extends around the base's inner wall, in order to help protect the top of the base's inner wall from inadvertent contamination when the lid is removed. Disposable paper filters are sealed over the vents inside the lid and base by cooperating filter paper sealing flanges provided in the filter papers' retainers, lid and base, in order to maintain the sterility of the contents of the sterilization container system after sterilization. Dual disc filter paper retainers provide non-aligned vents which prevent tearing or puncturing of the filter papers by the instruments being sterilized. Alignment cams on the base ensure proper alignment of lid and base for a good seal therebetween. The instrument basket inside the sterilization container system has a base elevated above the filter paper retainer to permit free circulation of the sterilizing media. Support feet on the base elevate the instrument basket above the bottom of the base to prevent condensation from being trapped within the sterilization container system.