An electrostatic accelerator, Tandetron (Model 4117MC, High Voltage Engineering Europe Co.) was installed in National Institute of Radiological Sciences (NIRS) for PIXE (Particle Induced X-ray Emission) analysis in 1999. The accelerating voltage is 0.4 to 1.7MV, and the maximum beam current is 5microA at 3.4MeV. This system has three beam ports for different types of PIXE analysis, conventional, micro-beam and in-air. Normal PIXE line has two types of X-ray detecting device, Si (Li) and CdZnTe detectors detectable for elements from Na (Z=11) to U (Z=92). Fifteen samples can semi automatically be measured at one time with the optical beam size from 0.5 to 2.0 mm at 100 nA of the beam current. A quadruple triplet magnet (Model OM2000, Oxford Micro beams, Ltd.) attached to the other beam port produces a proton micro-beam of the square shape less than 1micron x 1micron. Micro-beam scanning PIXE analysis is carried out with this beam at 50pA current and scanning area up to 2.0mm square. The in-air PIXE analysis is performed using the third beam port.In this paper, we introduce micro-PIXE scanning system showing the ability to draw elemental maps in a spatial resolution of about 1 µm with analyses of fish scale, fish otolith, crocus pollen and micro organisms. Fine ring structure of a fish scale was observed using elemental mapping with proton micro-beam scanning. Pollen was analyzed as one example of single cell to demonstrate the elemental distribution. Fish scale and otolith seem to be a kind of time recorder like tree rings. And the elemental composition reflects the living condition. Therefore, fish scale and otolith are possible to be used as a biological indicator.3rd International Symposium on Nuclear Analytical Chemistry (NAC-III
