Method of using an aseptic manipulation system, the aseptic manipulation system comprising an aseptic manipulation chamber, the inside of which is kept in an aseptic condition, and a decontamination chamber provided for removing microbes adhering to an object carried into the aseptic manipulation chamber from the outside thereof; the decontamination chamber having a first operation chamber provided with an inlet portion that can be closed, a second operation chamber connected to the first operation chamber and provided with an outlet portion that can be closed, and a closable communication portion for communicating between the first operation chamber and the second operation chamber, the decontamination chamber being connected to a pressure-adjusting mechanism adjusting the pressure of the first operation chamber and the second operation chamber, the first operation chamber and the second operation chamber being connected to a decontamination gas supply passage, which supplies decontamination gas, and an air supply and exhaust mechanism, which supplies clean gas, the air supply and exhaust mechanism forming said pressure-adjusting mechanism (51, 52, 53, 54, 85, 88, 95, 98); the method comprising: when the communication portion is open for communication between the first operation chamber and the second operation chamber, closing the inlet portion and the outlet portion, and generating an air current from the second operation chamber to the first operation chamber by the pressure-adjusting mechanism (51, 52, 53, 54, 85, 88, 95, 98); and when an object is carried into the aseptic manipulation chamber from the outside thereof, storing the object in the first operation chamber to undergo a first decontamination, in which the decontamination gas is supplied to the first operation chamber to act on the object carried into the aseptic manipulation chamber and inner walls of the first operation chamber, then moving the object from the first operation chamber to the second operation chamber through the communication portion to undergo a second decontamination in the second operation chamber, in which clean gas is supplied to the second operation chamber to remove the decontaminants from the object, and then carrying the object into the aseptic manipulation chamber. the decontamination chamber having a first operation chamber provided with an inlet portion that can be closed, a second operation chamber connected to the first operation chamber and provided with an outlet portion that can be closed, and a closable communication portion for communicating between the first operation chamber and the second operation chamber, the decontamination chamber being connected to a pressure-adjusting mechanism adjusting the pressure of the first operation chamber and the second operation chamber, the first operation chamber and the second operation chamber being connected to a decontamination gas supply passage, which supplies decontamination gas, and an air supply and exhaust mechanism, which supplies clean gas, the air supply and exhaust mechanism forming said pressure-adjusting mechanism (51, 52, 53, 54, 85, 88, 95, 98); the method comprising: when the communication portion is open for communication between the first operation chamber and the second operation chamber, closing the inlet portion and the outlet portion, and generating an air current from the second operation chamber to the first operation chamber by the pressure-adjusting mechanism (51, 52, 53, 54, 85, 88, 95, 98); and when an object is carried into the aseptic manipulation chamber from the outside thereof, storing the object in the first operation chamber to undergo a first decontamination, in which the decontamination gas is supplied to the first operation chamber to act on the object carried into the aseptic manipulation chamber and inner walls of the first operation chamber, then moving the object from the first operation chamber to the second operation chamber through the communication portion to undergo a second decontamination in the second operation chamber, in which clean gas is supplied to the second operation chamber to remove the decontaminants from the object, and then carrying the object into the aseptic manipulation chamber. when the communication portion is open for communication between the first operation chamber and the second operation chamber, closing the inlet portion and the outlet portion, and generating an air current from the second operation chamber to the first operation chamber by the pressure-adjusting mechanism (51, 52, 53, 54, 85, 88, 95, 98); and when an object is carried into the aseptic manipulation chamber from the outside thereof, storing the object in the first operation chamber to undergo a first decontamination, in which the decontamination gas is supplied to the first operation chamber to act on the object carried into the aseptic manipulation chamber and inner walls of the first operation chamber, then moving the object from the first operation chamber to the second operation chamber through the communication portion to undergo a second decontamination in the second operation chamber, in which clean gas is supplied to the second operation chamber to remove the decontaminants from the object, and then carrying the object into the aseptic manipulation chamber.