A microparticle analysis system comprising: a flow cytometer; and a 3D data analysis apparatus, wherein the 3D data analysis apparatus comprises: a data storage unit adapted to store measurement data of microparticles; an input unit adapted to select three kinds of variables independent of the measurement data; a data processing unit adapted to calculate positions and graphics in a coordinate space with the three kinds of variables being coordinate axes and to create a 3D stereoscopic image that represents a characteristic distribution of the microparticles; and a display unit adapted to display the 3D stereoscopic image, the 3D data analysis apparatus being adapted to perform gating by variably setting a separate area in the coordinate space on the basis of an input signal from the input unit and displaying the separate area in the 3D stereoscopic image, wherein the separate area is set along a track of an internal space of a pointer moved in the coordinate space, so that the internal space thereof passes through the area where the graphics corresponding to the microparticles to be analyzed exist and entirely or partially matching the area with the track of the internal space of the pointer. a flow cytometer; and a 3D data analysis apparatus, wherein the 3D data analysis apparatus comprises: a data storage unit adapted to store measurement data of microparticles; an input unit adapted to select three kinds of variables independent of the measurement data; a data processing unit adapted to calculate positions and graphics in a coordinate space with the three kinds of variables being coordinate axes and to create a 3D stereoscopic image that represents a characteristic distribution of the microparticles; and a display unit adapted to display the 3D stereoscopic image, the 3D data analysis apparatus being adapted to perform gating by variably setting a separate area in the coordinate space on the basis of an input signal from the input unit and displaying the separate area in the 3D stereoscopic image, wherein the separate area is set along a track of an internal space of a pointer moved in the coordinate space, so that the internal space thereof passes through the area where the graphics corresponding to the microparticles to be analyzed exist and entirely or partially matching the area with the track of the internal space of the pointer. a data storage unit adapted to store measurement data of microparticles; an input unit adapted to select three kinds of variables independent of the measurement data; a data processing unit adapted to calculate positions and graphics in a coordinate space with the three kinds of variables being coordinate axes and to create a 3D stereoscopic image that represents a characteristic distribution of the microparticles; and a display unit adapted to display the 3D stereoscopic image, the 3D data analysis apparatus being adapted to perform gating by variably setting a separate area in the coordinate space on the basis of an input signal from the input unit and displaying the separate area in the 3D stereoscopic image, wherein the separate area is set along a track of an internal space of a pointer moved in the coordinate space, so that the internal space thereof passes through the area where the graphics corresponding to the microparticles to be analyzed exist and entirely or partially matching the area with the track of the internal space of the pointer.