It was difficult for allophane to determine its chemical structure by simple application of conventional structure analysis like X-ray diffraction method, because of the poorly ordered nature in its structure. However, dexterous and extensive utilization of various chemical procedures and recent sophisticated instrumental analysis such as solid-state high resolution NMR spectroscopy has made almost clear the chemical structure of allophane. The clarified structure has enabled allophane to elucidate its physicochemical properties, ion exchange and adsorption, charge characteristics, dispersion and flocculation, interaction with water molecule and so forth, in the stage of as deep as molecular level. It is expected that more detailed mechanism of the properties in microscopic and electron levels will be analyzed by active introduction of new computer methods, molecular orbital calculation, with which distribution and energy for the orbital of allophane structure and charge allocation as well can be evaluated. In the near future, academic fields of “quantum clay mineralogy” and “quantum soil science” may necessarily be born and developed, just as molecular biology and quantum biology have been occurred.