A micro-PIXE analysis system based on the ion beam analysis system by Oxford Microbeams Ltd. has been developed at the NIRS-electrostatic accelerator facility. The introduction of the CdTe X-ray detector dramatically improved the detection efficiencies for heavy elements that are important in the life sciences and environmental science. This system has been used for various projects and has provided several meaningful results, thus establishing the micro-PIXE system as an effective tool for the determination of elemental distribution with a high spatial resolution. In this paper, outline of the features of the micro-PIXE system at NIRS along with its recent application in research are introduced.