A sample preparation apparatus for a sample including an analyte containing epithelial cells of a uterine cervix collected from a subject, comprising: an ultrasonic vibrating unit including a liquid holding part which is configured to hold a liquid and an ultrasonic transducer which is configured to generate ultrasonic vibration, wherein the ultrasonic transducer is configured to apply ultrasonic vibration to the sample held in a measurement sample container through the liquid, and the ultrasonic vibrating unit is configured to reduce the degree of aggregation of the cells in the sample by applying the ultrasonic vibration; a container transporting unit which is configured such that in a raised position the container transporting unit can transport the measurement sample container holding the sample including the analyte from the ultrasonic vibrating unit to a sample preparation unit, and in a lowered position the container transporting unit is set so that the measurement sample container is immersed in the liquid held in the liquid holding part so that the surface of the sample in the measurement sample container is positioned lower than the surface of the liquid in the liquid holding part; the sample preparation unit which is configured to prepare a measurement sample by mixing the sample including the analyte to which the ultrasonic vibration is applied and a predetermined reagent; and a preparation control unit configured to control the ultrasonic vibrating unit to perform a separation process of the aggregated cells, to control the container transporting unit to move the measurement sample container to a predetermined position in the ultrasonic vibrating unit and immerse a part of the container in the liquid, and to control the container transporting unit to move the measurement sample container to the sample preparation unit. an ultrasonic vibrating unit including a liquid holding part which is configured to hold a liquid and an ultrasonic transducer which is configured to generate ultrasonic vibration, wherein the ultrasonic transducer is configured to apply ultrasonic vibration to the sample held in a measurement sample container through the liquid, and the ultrasonic vibrating unit is configured to reduce the degree of aggregation of the cells in the sample by applying the ultrasonic vibration; a container transporting unit which is configured such that in a raised position the container transporting unit can transport the measurement sample container holding the sample including the analyte from the ultrasonic vibrating unit to a sample preparation unit, and in a lowered position the container transporting unit is set so that the measurement sample container is immersed in the liquid held in the liquid holding part so that the surface of the sample in the measurement sample container is positioned lower than the surface of the liquid in the liquid holding part; the sample preparation unit which is configured to prepare a measurement sample by mixing the sample including the analyte to which the ultrasonic vibration is applied and a predetermined reagent; and a preparation control unit configured to control the ultrasonic vibrating unit to perform a separation process of the aggregated cells, to control the container transporting unit to move the measurement sample container to a predetermined position in the ultrasonic vibrating unit and immerse a part of the container in the liquid, and to control the container transporting unit to move the measurement sample container to the sample preparation unit.