This work describes the use of supercrifical CO2 for the inactivation of the natural microflora of a cocoa product while the cocoa butter is extracted. Different parameters have been explored in the yield of both operations, including the operation conditions, the addition of ethanol and hydrogen peroxide, the use of pressure cycles, the humidification of the raw material, and the solvent ratio. The impact of the procedure was analyzed in the total content of polyphenols as well as on the flavanol fraction because these compounds gave functional properties to the product. The extraction operation was benefited by the use of high pressure and solvent ratios as well as by the use of ethanol as co-solvent. Temperature had to be counterbalanced to facilitate the natural microflora inactivation. Only by the combination of moderate temperature (65-80 degrees C) and the addition of small amounts of water (less than 10%), it was possible to fully eliminate the thermo-resistant spores that contaminated the product, since the application of pressure cycles and the addition of hydrogen peroxide or ethanol were useless. The method served also in fungi spores that were artificially inoculated in the product. The defatted product preserved its polyphenol content after the treatment. The equilibrium solubility of the butter in the CO2 was obtained from the extraction curves and compared to previous published data. (c) 2007 Elsevier B.V All rights reserved.