The effects of polyphenol removal from common buckwheat seed flours with cold aqueous organic solvents (including 95% ethanol, 70% 2-propanol, and 80% methanol, v/v) on the physicochemical and conformational properties of their protein isolates (BPI) were investigated. The extraction resulted in considerable reduction in its polyphenol content, especially protein-bound polyphenol content, and concomitant increase in its protein content. The efficiency of the removal of the polyphenols was much better in the 2-propanol case than in other two cases. The surface hydrophobicity of the proteins changed slightly, while the disulfide bond contents remarkably increased, partially at the expense of free sulfhydryl group contents. The protein solubility in the pH range of 7.0-11.0 and the proportion of undenatured globulins in BPI products were variably improved by the organic solvent extraction, and the extent of the improvements was highest in the 2-propanol case. Intrinsic emission fluorescence and far-UV and/or near-UV CD spectra showed that polyphenol removal resulted in significant changes in tertiary and/or secondary conformations of the proteins in BPI, and the changes were also related to the efficiency of the removal of the polyphenols. These results suggest that the physicochemical and conformational properties of BPI are closely related to its polyphenol level, and there is also a close relationship between its physicochemical properties and tertiary and/or secondary conformations.