The electronic structure of impurities, intrinsic defects and metamict areas has been studied in ZrSi04, Si02 и Zr02. Non empirical cluster MO LKAO of Xa-method of discrete variation has been used; energy spectrum, electronic configurations, effective charges of atoms, total and deformation electron density maps have been performed. The possibilities of the method for investigation of the real minerals with high structural disordering are discussed.