A systematic investigation of the property of the SDS-protein complex and the influence of the detergent sodium doedecyl sulphate (SDS) on protein purification is reported. The data demonstrate that SDS in the sample doesn't disturb gel permeation and hydro xyapatite chromatographic separation, but reduces the separation efficiency and protein recovery in hydrophobic interaction, affinity and reversed-phased chromatographic methods. A successful separation of many membrane and inclusion body proteins in genetic engineering will therefore require new concepts in column design as well as critical revision of the choice of mobile phases. This study provides important data on membrane and inclusion body proteins purification.