A lyophilization device configured for use in a lyophilization process has a body defining a chamber for receiving a liquid to be lyophilized, and a stopper creating a liquid-tight seal between the chamber and ambient atmosphere to form a sealed, empty sterile chamber. The stopper is adapted so that the chamber may be sterile filled with the substance through the stopper. A fluid passageway is formed through the stopper, through which the chamber is evacuated. The substance is lyophilized, the fluid passageway is closed, and the lyophilized substance is hermetically sealed within the chamber.