We have developed “micron-CT”, using micro-PIXE for in-vivo imaging. This system comprises an X-ray CCD camera (Hamamatsu photonics C8800X9) with high resolution (pixel size: 8×8μm2, number of pixels: 1000×1000) and an X-ray-point-source with a spot size of 1.5×1.5μm2 which is generated by irradiation of a microbeam on a pure metal target. Thus we can acquire projection data with high resolution. The sample is placed in a small diameter tube and is rotated by a stepping motor. The 3D images were reconstructed from the obtained projection data by using cone-beam CT reconstruction algorithm. X-ray spectra produced by heavy charged particle bombardment, exhibit a much smaller continuous background compared to electron bombardment. Therefore, X-rays produced by ion beam can be used as a monochromatic and low energy X-ray source. The feature is very effective to investigate small insects. Moreover we can get elemental distribution image of object by choosing appropriate characteristic X-rays corresponding to the absorption edge. On the other hand, the conventional X-ray CT, in which continuous X-rays are used, provides images of the electron density in the object. Using this system, we were able to get 3D images of a living ant's head with 6 μm spatial resolution. By using Fe-K-X-rays (6.40 keV) and Co-K-X-rays (6.93 keV), we can investigate the 3D distribution of Mn (K-absorption edge = 6.54 keV) in an ant's head.