To understand the possible mechanism controlling the formation of silicon bodies in higher plants, we need to know the nature of organic compounds associated with silicon bodies and induces silicon precipitation in plant cells. A new method was developed to isolate pure silicon body in fresh leaves of rice (Oryaa sativa L. Var. 297) at low temperature by grinding and centrifugation procedures, which avoided degradation of organic molecules induced by high temperature and strong oxidizing acids used in the traditional method. The energy dispersive X-ray spectrum under scanning electron microscope showed that there was a great amount of carbon in silicon bodies in addition to silicon and oxygen. Organic compounds intimately associated with silicon bodies were released by treatment with HF solution. Analysis of the organic compounds by micro-infrared spectroscopy revealed the presence of polyphenol and polysaccharide and a little protein.