A medical instrument sterilization system and method is provided. The system includes a sterilization container having a first container portion engagable with a second container portion to enclose an interior compartment from an exterior atmosphere. At least one insert is locatable within the interior compartment of the sterilization container, the at least one insert having a medical instrument holding area surrounded by a plurality of sidewalls, wherein the medical instrument holding area is sized to hold at least one medical instrument. A filter is secured within a wall of the first container portion, wherein the filter is in communication with the interior compartment and the exterior atmosphere.
