The effects of ionic strength and multivalent metal ions on the flocculation performance in Escherichia coli cell disintegrates using the polycationic chitosan as a flocculant were investigated. The study showed that ionic strength could be used to optimize the selectivity in flocculation. The best selectivity was obtained at 0.5 M sodium chloride where 95% of the cell debris and 88% of the nucleic acids could be removed from the disintegrate by sedimentation, leaving 99% of proteins and 86% of -galactosidase enzyme activity in clarified solution. We will also discuss the mechanisms for interaction between chitosan and different groups of components in the disintegrate: cell debris particles, nucleic acid polymers and proteins.