An aseptic manipulation system, comprising: an aseptic manipulation chamber, the inside of which is kept in an aseptic condition; and a decontamination chamber provided at the inlet side of the aseptic manipulation chamber; wherein a decontamination medium is supplied from a decontamination gas supply device to the decontamination chamber in order to remove microbes adhering to an object introduced into the aseptic manipulation chamber from the outside thereof; characterized in that the decontamination chamber has 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, a communication portion communicating between the first chamber and the second chamber and being able to close, an inlet portion closing mechanism for closing the inlet portion, an outlet portion closing mechanism for closing the outlet portion, and a communication portion closing mechanism for closing the communication portion; the aseptic manipulation system further comprising: a first ventilation mechanism (51, 53, 85, 95) ventilating the inside of the first operation chamber; a second ventilation mechanism (52, 54, 88, 98) ventilating the inside of the second operation chamber; and a control unit monitoring the open-closed states of the inlet portion closing mechanism, the outlet portion closing mechanism, and the communication portion closing mechanism, the control unit controlling the operations of the first ventilation mechanism (51, 53, 85, 95) and the second ventilation mechanism (52, 54, 88, 98); the control unit ventilating the inside of the first operation chamber with the first ventilation mechanism (51, 53, 85, 95) for more than a first specified number of times so that the inside of the first operation chamber can be communicated with the inside of the second operation chamber, after an object is introduced into the first operation chamber from the outside and the inlet portion is closed while the communication portion is closed, and the control unit ventilating the inside of the second operation chamber with the second ventilation mechanism (52, 54, 88, 98) for more than a second specified number of times, which is greater than the first specified number of times, after the object is transferred into the second operation chamber from the first chamber and the communication portion is closed while the outlet portion is closed. an aseptic manipulation chamber, the inside of which is kept in an aseptic condition; and a decontamination chamber provided at the inlet side of the aseptic manipulation chamber; wherein a decontamination medium is supplied from a decontamination gas supply device to the decontamination chamber in order to remove microbes adhering to an object introduced into the aseptic manipulation chamber from the outside thereof; characterized in that the decontamination chamber has 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, a communication portion communicating between the first chamber and the second chamber and being able to close, an inlet portion closing mechanism for closing the inlet portion, an outlet portion closing mechanism for closing the outlet portion, and a communication portion closing mechanism for closing the communication portion; the aseptic manipulation system further comprising: a first ventilation mechanism (51, 53, 85, 95) ventilating the inside of the first operation chamber; a second ventilation mechanism (52, 54, 88, 98) ventilating the inside of the second operation chamber; and a control unit monitoring the open-closed states of the inlet portion closing mechanism, the outlet portion closing mechanism, and the communication portion closing mechanism, the control unit controlling the operations of the first ventilation mechanism (51, 53, 85, 95) and the second ventilation mechanism (52, 54, 88, 98); a first ventilation mechanism (51, 53, 85, 95) ventilating the inside of the first operation chamber; a second ventilation mechanism (52, 54, 88, 98) ventilating the inside of the second operation chamber; and a control unit monitoring the open-closed states of the inlet portion closing mechanism, the outlet portion closing mechanism, and the communication portion closing mechanism, the control unit controlling the operations of the first ventilation mechanism (51, 53, 85, 95) and the second ventilation mechanism (52, 54, 88, 98); the control unit ventilating the inside of the first operation chamber with the first ventilation mechanism (51, 53, 85, 95) for more than a first specified number of times so that the inside of the first operation chamber can be communicated with the inside of the second operation chamber, after an object is introduced into the first operation chamber from the outside and the inlet portion is closed while the communication portion is closed, and the control unit ventilating the inside of the second operation chamber with the second ventilation mechanism (52, 54, 88, 98) for more than a second specified number of times, which is greater than the first specified number of times, after the object is transferred into the second operation chamber from the first chamber and the communication portion is closed while the outlet portion is closed.